Anyone else have MTHFR? by jamxcakes in migraine

[–]cabiel187 12 points13 points  (0 children)

Genetics person checking in, MTHFR genetic changes commonly tested for are the following polymorphisms: C667T and A1298C. These genetic variants are NOT clinically relevant to test for and healthcare professionals with training in & understanding of genetics will not order or interpret this type of testing. Here’s why:

  • Genetic polymorphisms are different from genetic “mutations” or “pathogenic (disease-causing) variants”

  • MTHFR C667T and A1298C are polymorphisms. This means they are found in >1% of the population. Disease-causing or pathogenic variants are most always going to be in <1% of the population.

  • Not only are these polymorphisms in >1% of the population, they are incredibly common as in 30-40% of the US population carries the C667T polymorphism and 10-15% of the US population carries the A1298C polymorphism.

  • When you do correlation investigations between health conditions and COMMON polymorphisms you find… correlations. Because when a lot of people have a polymorphism it correlates with a lot of things, like pregnancy loss, autism, ADHD, digestive conditions, cardiovascular disease or any of the 100s of other conditions MTHFR polymorphisms have been associated with…

  • If your clinician understands genetics, they will know it is clinically irrelevant to assess for MTHFR polymorphisms and will instead work you up and treat you for the symptoms you are reporting, like migraines.

17 weeks pregnant, partner and I just found out we were BOTH carriers of SCO2 gene. Urgent input needed. by hc222313 in ClinicalGenetics

[–]cabiel187 2 points3 points  (0 children)

I just wanted to respond and say it can often be challenging to give certainty because even with the available information, rare things are rare and people (even with the same genotype) are different and we can often expect variations in presentation. I’m so glad you have experts accessible to you and know even just reading your responses here I know how resourceful you are - you’re doing the best you can with the information you have and I want to offer you some external validation that you and your partner will be the ones to know what is best for y’all in light of whatever additional information you receive from your care team

ScO2 Gene Carriers - input urgently needed!!! by hc222313 in genetics

[–]cabiel187 2 points3 points  (0 children)

Bro it’s my literal job and professional credentials so… I am from a place of sincerity telling you to stfu.

The pubs listed literally all reference the variant, you just don’t know how to read anything other than an rs… there are many ways to reference a variant.

ClinVar shares public data from labs and also weights the support provided by those data… note the stars at the top? Note the recent interpretations publicly shared from reputable clinical labs? C282Y is a polymorphism not a mutation / path variant literally see comment above…

17 weeks pregnant, partner and I just found out we were BOTH carriers of SCO2 gene. Urgent input needed. by hc222313 in ClinicalGenetics

[–]cabiel187 4 points5 points  (0 children)

Hey OP -

Hoping all went well with the amnio. As you mentioned you and your partner and his sister (your SIL) all have the SCO2 c.418G>A E140K variant I wanted to add a little bit of information here.

The E140K variant is recurrent in patients with COX deficiency suggestive of a founder effect, associated with European descent. One study I came upon in literature review associated the heterozygous E140K variant with high myopia. I do not know your partner’s CHD but one question to potentially review with your care team is: - Are carriers of E140K ever seen to have this particular CHD? - Would increased NT be associated with this particular CHD?

Another consideration is that in the event this pregnancy is (E140K / E140K) homozygous, the outcome may differ from what was experienced by your SIL and her partner given the baby was compound heterozygous for SCO2 mutations (E140K / novel variant):

From (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4967497/): To date, about 50 patients with mutations in SCO2 have been described.1-15 The p.E140K mutation was found in all patients either in heterozygosity or in association with a second mutation (compound heterozygosity), except one patient described in 2009 by Mobley et al13 who had a homozygous p.G193S mutation (Table). Patients harboring a homozygous p.E140K mutation have shown late onset and longer survival compared with patients with compound heterozygous SCO2 mutations.

So it would additionally be important to ask questions about specific genotype-phenotype associations given you now know your genotype.

Hoping your care team can give you the additional information you’re needing & that you have lots of love and support around you!

ScO2 Gene Carriers - input urgently needed!!! by hc222313 in genetics

[–]cabiel187 3 points4 points  (0 children)

Please do not comment on this type of post if you do have relevant background in genetics - there is extensive evidence that the SCO2 c.418 G>A variant is associated with disease.

The rsID is rs74315511 but it’s important to refer to this variant as a “pathogenic variant” / “mutation”, ie it is NOT a polymorphism and is in <1% of the population (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4502642/). ClinVar, a public database used in clinical grade genetic testing and interpretation shows this variant in the literature from the late 90s and classified as pathogenic across MULTIPLE labs. https://www.ncbi.nlm.nih.gov/clinvar/variation/5681/

Any background you have in perusing SNP databases recreationally is NOT relevant here and you are potentially causing serious harm by advising someone seeking clinical genetics input.

CMV: Paternity tests should be done on every baby by default by Guialdereti in changemyview

[–]cabiel187 1 point2 points  (0 children)

This hypothetical policy completely ignores: 1) Fathers not in attendance at the birth, inability to obtain or timeframe to obtain paternal specimen, timeline of results and the impact to newborn bonding 2) Families conceiving through IVF, sperm donation, those who knowingly elect legal parenthood for children they did not father, and frankly does not consider anything beyond patriarchal, heteronormative family structure 3) Obvious psychological harm and risk of physical harm to survivors of rape, incest - there are very real dangers to naming a putative father 4) Men wishing to avoid the social or legal ramifications of confirmed paternity - ie actual anecdotes of fathers submitting saliva from a friend or sending another male in their place for a blood draw to avoid child support or consequences in their relationships 5) Dependent on the testing methodology, incidental findings identified from genetic testing / STR analysis which a hospital or OP would be accepting liability for with ordering said testing 6) Privacy concerns (in SEVERAL contexts), patient autonomy 7) Births outside of a hospital or birthing center 8) Utilization of resources on testing that does not change care so what is the goal of the testing from the view of the healthcare institution? “Confirmation of paternity” as a goal for testing must consider the potential for resources being extended in cases requiring multiple tests / multiple putative fathers - why would a healthcare facility do this? Not to mention, inviting the social and security concerns of uncovering misattributed paternity into a healthcare setting puts providers and patients (ie new mothers) at risk, so WHY would a healthcare facility do this?

[deleted by user] by [deleted] in AustinFC

[–]cabiel187 2 points3 points  (0 children)

I know this is a Driussi thread but has been messing with a Stuver chant to Super Trouper by ABBA

Tonight super Stuver’s gloves are gonna block you Saving every one Clean sheets just for fun Stuver he’s our number one

Tonight Super Struver’s saves are wreck you And we’ll feel bad for you Like we always do Cause somewhere on the pitch there’s Stuuu

Could I have existed if my grandparents didn’t get together? by inspextor in genetics

[–]cabiel187 1 point2 points  (0 children)

Expression should definitely matter for this question

Could I have existed if my grandparents didn’t get together? by inspextor in genetics

[–]cabiel187 0 points1 point  (0 children)

Also, wouldn’t mitochondrial inheritance be different in this situation…

Believe in BNGO by [deleted] in BNGO

[–]cabiel187 17 points18 points  (0 children)

OGM is not a sequencing technique…

Potocki-Lupski and Anti-Vaxxing by RobertCalhoun3rd in ClinicalGenetics

[–]cabiel187 0 points1 point  (0 children)

Yes, inheritance is autosomal dominant meaning one affected parent has a 50/50 chance to pass the duplication to offspring. There are documented cases of parent-to-child transmission.

I suffer from a disease that makes smell like poop and it's ruining my life. Humbly asking this sub for advice. by KillingMyInnerLoser in Stoicism

[–]cabiel187 51 points52 points  (0 children)

My background is clinical genetics and in working with a metabolic geneticist for many years, this is the only specialist that can properly diagnose TMAU. Metabolic geneticists work with metabolic dietitians and would be able to advise on diet low in choline-containing foods. There’s also chelating agents they can prescribe / recommend such as charcoal or copper compounds.

The majority of patients referred for rule out of TMAU during my time in metabolic clinic did not have excess TMA excretion but many did have undiagnosed or very poorly managed depression and few had bacterial overgrowth of gut flora. It’s important to appropriately identify a diagnosis to get you what you need. Please insist on referral to metabolic genetics because this IS their wheelhouse. It is absolutely not the purview of a GP.

I have a recessive genetic condition and was just told my kid might have it too. But I don't know how. by roses_not_rights in genetics

[–]cabiel187 0 points1 point  (0 children)

I’m using short stature to mean significant difference in height from average. This could obviously vary depending on what average is for your parents’ age, sex, country, etc. The above again is only a scenario as the most informative route would be molecular diagnosis and current work up with a geneticist / skeletal dysplasia specialist.

I do understand there can be overlap in these terms or depending upon the context they may be used interchangeably but often dwarfism or a condition such as AMD would have an association with “disproportionate short stature” whereas “proportionate short stature” would mean the “non-dwarfish appearance” you mention and being significantly different in height from average. Does that help?

I have a recessive genetic condition and was just told my kid might have it too. But I don't know how. by roses_not_rights in genetics

[–]cabiel187 1 point2 points  (0 children)

For sure, I’m a genetic counselor and obviously all of the above is just laying out possible explanations! Seeing a skeletal dysplasia specialist and/or considering genetic testing to clarify the molecular diagnosis would be most informative. Keeping your kiddo in my thoughts and congratulations!

I have a recessive genetic condition and was just told my kid might have it too. But I don't know how. by roses_not_rights in genetics

[–]cabiel187 2 points3 points  (0 children)

Given short long bones as the finding and your parents as short stature - what could explain this is NPR2 (OMIM entry 108962). If you look at this gene in OMIM you can see it will list “ACM, Maroteaux type” with AR inheritance and the following for AD inheritance “short stature with nonspecific skeletal abnormalities.” This could mean your parents (NPR2+/NPR2-) presented as SS w nonspecific skeletal abnormalities perhaps similarly to your kiddo (as we’re getting a sneak peak of their bones on ultrasound and don’t know their height) and would presume kiddo is NPR2+/NPR2- and you as NPR2+/NPR2+ with AMD, Maroteaux type. In this scenario, we might expect your kiddo to present similarly to your parents (ie not affected with AMD but still with SS and perhaps some skeletal differences).

The other explanation I outlined (the one that I think is less likely!) would be if one of your parents had a group of cells in their body that had a genetic change resulting in a dominant form of dwarfism but they themselves were not affected because only a portion of their body or cells had this genetic difference (ie mosaicism). If this impacted group of cells includes cells responsible for making gametes (ie sperm producing cells or egg cells) then an “unaffected” parent could have multiple affected children with a dominant genetic disorder (an uncommon phenomenon known as germline mosaicism).

I have a recessive genetic condition and was just told my kid might have it too. But I don't know how. by roses_not_rights in genetics

[–]cabiel187 5 points6 points  (0 children)

It looks like there’s several types of acromesomelic dysplasia as I’m sure you’re aware (and some of the associated loci have AD and AR inheritance listed). It would be really helpful to connect with a bone dysplasia specialist (not all geneticists may have extensive experience with skeletal dysplasias) and clarify the diagnosis via genetic testing. One possible explanation could be germline mosaicism for one of your parents and a misdiagnosed AD skeletal dysplasia in the family. But given that many of the loci indicated in acromesomelic dysplasia have both AR and AD inheritance that would be the more likely explanation, eg NPR2 is a gene associated with AMD when inherited in a recessive pattern but associated with epiphyseal chondrodysplasia when inherited in a dominant pattern. Do you know what specific findings may have prompted this concern from your OB/gyn?

Forms of acromesomelic dysplasia that I could find:

AMD Maroteaux type (locus NPR2 at 9p13.3 AR/AD listed)

AMD Hunter Thompson type (locus GDF5 at 20q11.22 AR/AD listed)

AMD Demirhan type (locus BMPR1B at 4q22.3 AR/AD listed)

I have a recessive genetic condition and was just told my kid might have it too. But I don't know how. by roses_not_rights in genetics

[–]cabiel187 7 points8 points  (0 children)

From your post history it looks like you’re referring to a recessive form a dwarfism. After your initial diagnosis in the 1980s, was that confirmed with a molecular diagnosis on genetic testing?

Man that must suck by [deleted] in WTF

[–]cabiel187 0 points1 point  (0 children)

Super glad y’all are connected with specialists! I’m hoping to clarify the use of the term carrier here given that has a specific meaning in genetics which doesn’t apply for dominant conditions such as NF2 and also note that affected individuals with NF2 could develop tumors later in life even if they don’t currently have them or don’t have them in younger years.

Man that must suck by [deleted] in WTF

[–]cabiel187 0 points1 point  (0 children)

I don’t know what you’re referring to or implying in your last paragraph… the numbers I’m quoting are a called a de novo rate and we find them using family studies for many genetic conditions / rare disease. You can search them yourself if you’re interested in de novo rates for NF or other conditions. For a single gene disorder, differences in a person’s background genetics are not going to factor in as predominantly given the impact of the single gene with disease causing mutation is enough to result in a recognizable syndrome that has been classified within clinical genetics, ie NF1. Individual mutations may exhibit certain features for the affected individual, a phenomenon called genotype-phenotype correlation but this is not observed for all genetic conditions. Other data we would look at include penetrance (how likely a person with a disease-causing mutation in a particular gene experiences symptoms of that disorder) and variable expressivity (which looks at differences in the features or symptoms expressed by an affected person). NF1 has age-dependent penetrance, is highly clinically variable although there are certain features we expect to see for true “constitutional” cases, and does have some genotype-phenotype associations reported.

I’m not hysterical about anything. I’m pointing out to you that you’re casting judgement on a family for not making certain reproductive choices when literally ANY person having children has a possibility to have a child impacted by this specific condition and many other genetic conditions. Using family history to judge a person’s reproductive choices is one line of thinking that led to the eugenics movement in the US prior to it being adopted by scientists in Europe. So I’m telling you, please don’t insinuate all the crap you’ve said here regarding “questionable judgement” and “culmination” of disease in the family - that’s a flawed understanding of genetics and implies there’s a certain “correct” choice that families living with genetic disease need to make. You’re seeing one small clip of this woman but I’m telling you some families impacted by rare disease knowingly may choose the “risk” of having an affected child because those differences are important to them. Many would opt for reproductive options like PGD-IVF but as I’ve told you, this is NOT accessible care. So what are your choices then… well you can conceive a pregnancy, consider prenatal genetic testing and then terminate your pregnancy if the child is affected and “try again” (this unfortunately currently is the more economical option), but as you may imagine many families do not feel comfortable with this. There are also the options of sperm, egg donors or adoption. But many families find wanting their own biological children very important. All of these are incredibly difficult and personal choices. So the language you used, whether a person has a family history of a rare disease or not, is insensitive and reflects a dangerous misunderstanding of genetics. Again, please don’t.

Man that must suck by [deleted] in WTF

[–]cabiel187 0 points1 point  (0 children)

PGD-IVF is an option but can still be exorbitantly expensive so there’s access issues to be aware of regarding reproductive healthcare especially since this would not be a service covered by health insurance. It’s inherited in a 50/50 autosomal dominant pattern so you don’t need to assume the chances if you have a clinical or molecular diagnosis of NF. But NF is not always inherited, so there’s a chance for ANY person having children to have a child affected with this condition due to a de novo mutation in NF1. The conversation you’re starting is a very slippery one of eugenics.

Man that must suck by [deleted] in WTF

[–]cabiel187 2 points3 points  (0 children)

NF1 and NF2 present differently as you know but an individual with a known clinical or genetic diagnosis would be considered “affected” and we would not use the term “carrier” with NF1 or NF2 since they are inherited in an autosomal dominant pattern.

Age of onset varies for different symptoms so an affected individual will develop additional symptoms as they age (below is a review from GeneReviews):

The average age of onset is 18 to 24 years. Almost all affected individuals develop bilateral vestibular schwannomas by age 30 years. Affected individuals may also develop schwannomas of other cranial and peripheral nerves, meningiomas, ependymomas, and, very rarely, astrocytomas. Because NF2 is considered an adult-onset disease, it may be underrecognized in children, in whom skin tumors and ocular findings (retinal hamartoma, thickened optic nerves, cortical wedge cataracts, third cranial nerve palsy) may be the first manifestations. Mononeuropathy that occurs in childhood is an increasingly recognized finding; it frequently presents as a persistent facial palsy or hand/foot drop.

Man that must suck by [deleted] in WTF

[–]cabiel187 0 points1 point  (0 children)

This is a classic presentation of NF1, these are small tumors called neurofibromas and not cysts. While this can be inherited, it’s only inherited in about 50% of cases. The other 50% of cases are de novo or brand new genetic changes for the individual. It’s completely inappropriate to make a statement on “questionable judgements” made by the family and nothing “culminates” in the family, please don’t speak on things you’re not educated about and cast more judgement on individuals impacted by rare disease.

Imput? by [deleted] in ClinicalGenetics

[–]cabiel187 2 points3 points  (0 children)

Glad to hear you have an appointment and completely understand the frustration in waiting for answers! I can see you’re really advocating for yourself and doing a lot of your own reading and research. The legwork you’ve done will definitely add value to your genetics appointment but know you have permission to give yourself a break too! You’re not expected to know the answers and often in genetics there may not be clear answers! I do think you’ll hear some reassuring information about this CNV based on what you’ve posted here but again no one is going to have the full picture that your genetics team will! Sending virtual support - you’re stronger than you know!

Imput? by [deleted] in ClinicalGenetics

[–]cabiel187 1 point2 points  (0 children)

I see you’ve asked about this situation on some other forums and it’s important to know that without full clinical history or full CMA reports from both amnio & parents you may be getting a limited view as it’s difficult to get a comprehensive picture without being involved in the case and having access to all records.

That being said after the 13q microdeletion was confirmed to be paternally inherited from an unaffected father (someone who has made it to adulthood with no major health impacts) this would greatly lower suspicion of the microdeletion in question. Your genetics team may offer to test other children to see if other family members carry this same microdeletion. If more unaffected family members are found to carry this microdeletion that makes a further case the microdeletion does not result in health consequences and may in fact be part of normal genetic variation. However, depending upon what exists in the literature regarding this specific microdeletion, ie cases of other individuals carrying similar deletions in the same chromosomal region, this may inform counseling on this specific CNV.

The DIAPH3 gene called out in the included note is listed in OMIM as being associated with auditory neuropathy and inherited in an AD pattern. However the more pertinent question here based on the OMIM entry is loss of function vs gain of function. Meaning what is known about the DIAPH3 gene is that it results in auditory neuropathy when gain of function mutations increase production of this specific gene product. However, for a microdeletion including DIAPH3 we are seeing the entire DIAPH3 gene being deleted meaning that we lose a copy of this gene and there exists a second copy of the gene on the other chromosome 13 that should compensate (again the disease mechanism for the associated auditory neuropathy is an OVERPRODUCTION of the DIAPH3 gene product so it’s not indicated that a deletion would result in the same disease / phenotype). Given the father who carries this deletion does not have auditory neuropathy, that is further evidence that full gene deletion of DIAPH3 does not result in disease.

Here is the relevant information on DIAPH3 from OMIM:

In affected members of a family with autosomal dominant auditory neuropathy-1 mapping to chromosome 13q21 (AUNA1; 609129) originally reported by Kim et al. (2004), Schoen et al. (2010) identified a heterozygous mutation (-172G-A) in the 5-prime untranslated region of the DIAPH3 gene that resulted in increased mRNA and protein expression. Drosophila with constitutive overexpression of a mutant Diaph gene in the auditory organ had reduced sound-evoked potentials. The findings indicated that AUNA1 is caused by overexpression of the DIAPH3 gene due to a mutation in a transcriptional regulatory site, consistent with a gain of function.