hu1A57E4 (genome_hu1A57E4_23andMe) - GET-Evidence variant report

Variant report for hu1A57E4 (genome_hu1A57E4_23andMe)

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VariantClinical
Importance
ImpactAllele
freq
Summary
1SERPINA1-E366KHighWell-establishedWell-established pathogenic

Recessive, Carrier (Heterozygous)
0.0117122This is also called the "Pi Z" or "Z" allele. When homozygous (acting in a recessive manner) this variant is the major cause of severe alpha-1-antitrypsin deficiency (95% of cases) which often leads to emphysema or chronic obstructive pulmonary disease (COPD) and liver disease in adults and children. Heterozygosity for this variant may also be associated with increased rate of lung or liver problems, especially when combined with another variant with reduced function (compound heterozygous).1
2COL9A3-R103WModerateLikelyLikely pathogenic

Dominant, Heterozygous
0.0480573Carriers of this collagen variant are associated with having a significantly increased risk of lumbar disc disease (~11% total risk compared to a typical risk of 4%). 1
3COL4A1-Q1334HLowLikelyLikely pathogenic

Dominant, Heterozygous
0.324689This common variant has been associated with arterial stiffness and, in Japanese, a small increased risk of myocardial infarction (MI, a.k.a. heart attack). This last observation supported a dominant effect for this variant and, assuming a lifetime risk of 15% for MI, we estimate carriers have an additional risk of 0.5-3%.1
4PRF1-A91VLowLikelyLikely pathogenic

Complex/Other, Heterozygous
0.0325339This variant may be associated with a slightly increased susceptibility to some rare blood disorders, in particular autoimmune proliferative disease, if combined with a more severe mutation elsewhere. Most reports lack statistical significance.1
5RET-R982CLowUncertainUncertain pathogenic

Dominant, Heterozygous
0.016174Initially suspected of causing Hirschsprung’s disease, this rare variant has been later reported as present in unaffected controls (allele frequency around 1%). Supporting a lack of effect: Panini et al. did not find loss of function effects seen in other variants, and Svensson et al. report unaffected relatives in a family who carried the same variant. OMIM lists it as reported to cause increased susceptibility, but there do not appear to be any statistically significant reports supporting this hypothesis.1
6RNASEL-R462QLowUncertainUncertain pathogenic

Complex/Other, Homozygous
0.278026Associated with increased risk of prostate cancer in individuals who already have a family history of prostate cancer, but studies have been unable to replicate this finding in sporadic (non-familial) prostate cancer cases.1
7SP110-L425SLowUncertainUncertain pathogenic

Unknown, Homozygous
0.863357This variant is associated with a slightly increased risk of tuberculosis. It is unclear whether it is itself causal, or in linkage disequilibrium with some other causal variant that has a stronger effect.1
8TP53-P72RLowUncertainUncertain pathogenic

Unknown, Homozygous
0.627743This is a common variant was first reported as a polymorphism. It has since had mixed associations with cancer: Storey et al. conclude a 7x *increased* risk of HPV cancer for homozygotes vs hets, but Jones et al. find a 1.98x *decreased* risk for colorectal cancer. This variant may have significant impact on particular cancers, but it is unclear what effect it has on the overall burden of cancer.1
9HFE-H63DLowUncertainUncertain pathogenic

Recessive, Carrier (Heterozygous)
0.109965There have been some hypotheses that this variant contributes to causing hereditary hemochromatosis, possibly as a compound heterozygote, but some others treat it as a polymorphism. Cys282Tyr is the classic causal variant and itself has very low penetrance. Mouse studies indicates this variant has a similar but weaker effect; if it has any effect at all its penetrance may be quite low and/or require modifier alleles.1
10WFS1-R611HLowUncertainUncertain not reviewed

Recessive, Carrier (Heterozygous)
0.400446This nonsynonymous SNP is associated with Wolfram Syndrome (known as DIDMOAD), which is characterized by early-onset non-autoimmune diabetes mellitus, diabetes insipidus, optic atrophy, and deafness) and to adult Type Two Diabetes Mellitus. The WFS1 gene maps to chromosome 4p16.3. The variant has been shown to be statistically associated with type II diabetes in six UK studies and one study of Ashkenazi Jews (Sandhu, M., et al., Minton et al.).1
11ADRB2-T164ILowUncertainUncertain pharmacogenetic

Unknown, Heterozygous
0.0109686This rare variant in β2-Adrenoceptor has only reported heterozygously (in 2-4% of the population) and strongly decreases the protein’s responsiveness to inducing compounds (agonists). Carriers of this variant are less sensitive to induction of increased heart rate, heart contraction, and vasodilation by β-AR agonists. Mixed data suggests that this variant does not have a significant impact on hypertension or heart disease. It may affect responsiveness to beta blocker drugs.1
12FUT2-W154XModerateWell-establishedWell-established protective

Recessive, Carrier (Heterozygous)
0.490519This recessive protective variant confers resistance to norovirus (which causes stomach flu). 20% of Caucasians and Africans are homozygous for this variant and are "non-secretors": they do not express ABO blood type antigens in their saliva or mucosal surfaces. Most strains of norovirus bind to these antigens in the gut, and so this non-secretor status confers almost total resistantance to most types of norovirus. There are notable exceptions, some strains of norovirus bind a different target and are equally infectious for secretors and non-secretors.1
13PRNP-M129VLowWell-establishedWell-established protective

Complex/Other, Heterozygous
0.339561This variant is associated with some protective effects for prion disease -- individuals homozygous for this variant are less susceptible to Creutzfeldt-Jakob, and Papua New Guinea individuals heterozygotes at this site are less susceptible to kuru. 1
14NPC1-H215RLowLikelyLikely protective

Complex/Other, Heterozygous
0.295687This variant is associated with a reduced risk of obesity, with an additive effect of -0.084 BMI per allele (an average of 0.54 pounds less, per allele, in a 5'6" individual). 1
15KCNJ11-K23ELowLikelyLikely protective

Unknown, Homozygous
0.738148This variant is associated with decreased risk of type 2 diabetes. It is unclear whether this variant has additive effects, or acts in a dominant or recessive manner. Assuming diabetes has a lifetime risk of 36%, we estimate a decreased risk of around 1-2% per copy of this variant.1
16TOR1A-D216HLowLikelyLikely protective

Unknown, Heterozygous
0.102993This SNP has been shown to be benign and play a protective role against Dystonia. 1
17BRCA2-T1915MLowUncertainUncertain protective

Unknown, Heterozygous
0.0205429Serrano-Fernández et al. found this variant to be associated with a modest (OR = 1.61) but significant (P = 0.0007) reduction in breast cancer risk. 1
18MLH1-I219VLowUncertainUncertain benign

Dominant, Heterozygous
0.239822Computational evidence, functional assays, and case/control studies suggest this variant is probably benign.1
19APOB-Y1422CLowUncertainUncertain benign

Unknown, Homozygous
0.999628This position is almost certainly an error in the HG18 reference sequence. 1
20FAH-R341WLowUncertainUncertain benign

Recessive, Carrier (Heterozygous)
0.0172895This variant shows pseudodeficiency for production of FAH protein which is connected with hereditary tyrosinemia type I. Pseudodeficiency was confirmed with site-directed mutagenesis and expression in a rabbit reticulocyte lysate system. The allelic frequency in 516 Norwegian controls was 0.022. 1
21DSPP-R68WLowUncertainUncertain benign

Unknown, Heterozygous
0.143045Probably benign. One report linked this to causing dentinogenesis Imperfecta type II in a large Swedish family, but subsequent publications have observed this is a common variant and conclude it is a nonpathogenic polymorphism.1
22TPCN2-G734ELowUncertainUncertain benign

Unknown, Homozygous
0.286166Pigmentation allele.1
23TCIRG1-R56WLowUncertainUncertain benign

Unknown, Heterozygous
0.0441778Probably benign. One publication implicates the variant in causing osteopetrosis, but this is contradicted by the relatively high allele frequency for the variant in Caucasians (5%, 1 in 400 homozygous) while that disease is extremely rare (1 in 250,000).1
24RP1-N985YLowUncertainUncertain benign

Unknown, Homozygous
0.348671Probably benign. One report linked this variant to high triglycerides, but a later paper found a nearby SNP with similar association and suggests that both findings are caused by linkage to an undiscovered causal variant.1
25SLC45A2-L374FLowUncertainUncertain benign

Unknown, Heterozygous
0.691764Pigmentation allele for non-black hair, and consequently, possible increased susceptibility to malignant melanoma.1
26MAPT-R370WLowUncertainUncertain benign

Unknown, Heterozygous
0.155549Probably benign.1
27PCSK9-G670ELowUncertainUncertain benign

Unknown, Homozygous
0.888269This variant is likely benign. 1
VariantPrioritization scoreAllele
freq
Num of
articles
Zygosity and Prioritization Score Reasons

Gene search

"GENE" or "GENE A123C":

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