hu474789 - GET-Evidence variant report

Variant report for hu474789

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VariantClinical
Importance
ImpactAllele
freq
Summary
1RYR2-G1886SHighUncertainUncertain pathogenic

Recessive, Carrier (Heterozygous)
0.0613424Reported to cause arrhythmogenic right ventricular cardiomyopathy when compound heterozygous with G1885E, although this finding is weakened after correcting for multiple hypotheses and it is unclear what penetrance such a genotype might have, if it is causal.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
3CFTR-S1235RModerateUncertainUncertain pathogenic

Recessive, Carrier (Heterozygous)
0.00529838Reported to cause mild dysfunction of the cystic fibrosis gene, it may result in cystic fibrosis when combined with more severe variants.1
4MTRR-I49MLowLikelyLikely pathogenic

Recessive, Homozygous
0.451199This common variant (HapMap allele frequency of 31.3%) in a protein involved in folate (B9) and cobalamin (B12) metabolism and is often reported as "MTRR I22M" (an alternative transcript position). Mothers homozygous for this variant are associated with having around a increased chance of a child with Down syndrome (risk of 0.4%, average risk in population is 0.25%). Notably, age plays a far larger role in the rate of Down syndrome (risk is 4.5% for a mother 45-years-of-age), and it is unknown how this variant may combine with the effect of age. There are conflicting reports associating this variant with incidence of neural tube defects, possibly when combined with MTHFR A222V.1
5NOD2-R702WLowLikelyLikely pathogenic

Complex/Other, Heterozygous
0.0334821NOD2 encodes a protein involved in bacterial recognition. This variant is associated with Crohn's disease in European populations, but not in Korean or Japanese groups.1
6CETP-A390PLowLikelyLikely pathogenic

Unknown, Heterozygous
0.0388548This variant is associated with slightly lower HDL (good) cholesterol, although it has a negligible effect (around 2 mg/dl).1
7WFS1-R611HLowUncertainUncertain not reviewed

Recessive, Homozygous
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
8TLR5-R392XLowUncertainUncertain pathogenic

Complex/Other, Heterozygous
0.0439673This variant is believed to impair the ability to generate an immune response to the flagella of the bacteria. It is weakly associated with an increased incidence of Legionnaires' Disease, p = 0.085, increased lifetime risk of disease ~0.88% (about twice average). The variant is also weakly associated with a reduced incidence of systemic lupus erythematosus, p = 0.165.1
9ELAC2-S217LLowUncertainUncertain pathogenic

Complex/Other, Heterozygous
0.273471Reported to be associated with increased susceptibility to prostate cancer, but later studies weaken the hypothesis. Xu et al.'s meta-analysis concludes that there is a small but significant increased risk (OR = 1.13). Assuming a lifetime risk of 16% for prostate cancer we calculate this leads to an increased risk of ~1.5% (17.5% total).1
10TGIF1-P83ShiftLowUncertainUncertain pathogenic

Complex/Other, Heterozygous
0.138889Severe variants in this gene are associated with holoprosencephaly disorders when combined with loss-of-function variants in SHH. Haploinsufficiency was identified in some families with this condition. It is unclear how likely this variant is to occur in combination with an SHH variant, or what phenotypic effect the variant would have on its own.1
11SP110-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
12H6PD-R453QLowUncertainUncertain pathogenic

Recessive, Carrier (Heterozygous)
0.308886This common variant may have a small pathogenic effect by contributing to cortisone reductase deficiency (a rare abnormality) when homozygous and combined with a serious pathogenic variant. The same authors have tested and ruled out a contribution to polycystic ovary syndrome (similar phenotype, more common disease).1
13TP53-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
14rs1544410LowUncertainUncertain pharmacogenetic

Unknown, Heterozygous
0.351562rs1544410 is a Vitamin D Receptor (VDR) single nucleotide polymorphism. It is unlikely that it has functional significance because it is located in an intron (Liu et. al.), but it is in strong linkage disequilibrium with rs731236 (Dvornyk et al), which is located in an exon. 1
15ABCC6-R1268QLowUncertainUncertain pharmacogenetic

Unknown, Homozygous
0.218907This common polymorphism appears to not have a significant phenotypic impact. A few studies report weak but significant associations with plasma lipids (in Inuits) and thalidomide toxicity.1
16FUT2-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
17CFH-V62ILowLikelyLikely protective

Complex/Other, Heterozygous
0.391616Associated with a decreased risk for age related macular degeneration (ARMD). Homozygotes for this have a 4-5% decreased attributable risk (3-4% vs. average 8% risk), heterozygotes have slightly lower than average risk (7%). Non-carriers have an increased risk (12-13%). ARMD impairs sharp vision as age progresses. While there is no cure, treatment can slow progression of the disease and environmental factors (smoking and obesity) contribute to higher risk.1
18NPC1-H215RLowLikelyLikely protective

Complex/Other, Homozygous
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
19KCNJ11-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
20CACNA1S-L458HLowLikelyLikely benign

Unknown, Heterozygous
0.27282Common polymorphism1
21COL9A2-T246MLowLikelyLikely benign

Unknown, Heterozygous
0.0252835Probably benign.1
22FLT4-N149DLowLikelyLikely benign

Unknown, Heterozygous
0.0725056Other severe variants in this gene are implicated in causing Milroy Disease (primary lymphedema) in a recessive manner. Although this variant is rare (2.3% allele frequency), it is still common enough that it is highly unlikely to have a severe, high penetrance pathogenic effect.1
23MLH1-I219VLowUncertainUncertain benign

Dominant, Heterozygous
0.239822Computational evidence, functional assays, and case/control studies suggest this variant is probably benign.1
24FBN2-S2580LLowUncertainUncertain benign

Dominant, Heterozygous
0.0779885Probably benign -- initially associated with congenital contractual arachnodactyly, but later reports classify it as a nonpathogenic polymorphism.1
25TYR-S192YLowUncertainUncertain benign

Unknown, Heterozygous
0.270682This variant is reported to affect skin pigmentation. It is associated with lighter skin in South Asians (OR 4-5) and with a lack of freckles in Europeans (OR 1.3).1
26DSPP-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
27APOB-Y1422CLowUncertainUncertain benign

Unknown, Homozygous
0.999628This position is almost certainly an error in the HG18 reference sequence. 1
28TPCN2-G734ELowUncertainUncertain benign

Unknown, Homozygous
0.286166Pigmentation allele.1
29FAH-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
30TAS2R38-A49PLowUncertainUncertain benign

Unknown, Heterozygous
0.431121This variant is strongly associated with causing the "taster" phenotype of phenylthiocarbamine (PTC) in a dominant manner.1
31PKP2-L366PLowUncertainUncertain benign

Unknown, Heterozygous
0.221231This variant is a benign polymorphism. 1
32PTCH1-P1315LLowUncertainUncertain benign

Unknown, Heterozygous
0.29631Common polymorphism, presumed benign.1
33SLC45A2-L374FLowUncertainUncertain benign

Unknown, Homozygous
0.691764Pigmentation allele for non-black hair, and consequently, possible increased susceptibility to malignant melanoma.1
34GUCY2D-A52SLowUncertainUncertain benign

Recessive, Carrier (Heterozygous)
0.21016One publication suggested that this variant possibly causes Leber's congenital amaurosis in a recessive manner, but the frequency data (36% in 1000 genomes) contradicts any significant pathogenic effect.1
35TAS2R38-I296VLowUncertainUncertain benign

Unknown, Heterozygous
0.463376This variant is associated with "taster" status of PTC, along with 49P and 262A. Due to linkage disequilibrium, the independent effects of positions 296 and 262 is unclear. The presence of 49P confers taster status in a dominant fashion, but in the absence of 49P, the presence of 262A/296V is still positively associated with tasting PTC.1
VariantPrioritization scoreAllele
freq
Num of
articles
Zygosity and Prioritization Score Reasons

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"GENE" or "GENE A123C":

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