hu428CA7 (BRB Exome Data) - GET-Evidence variant report

Variant report for hu428CA7 (BRB Exome Data)

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VariantClinical
Importance
ImpactAllele
freq
Summary
1PEX1-I696MHighUncertainUncertain pathogenic

Recessive, Carrier (Heterozygous)
0.0270547Reported as a mutation causing peroxisome biogenesis disorder in a single patient, presumably in a recessive manner.1
2PPARG-P12AModerateUncertainUncertain not reviewed

Unknown, Homozygous
0.08867821
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
4MBL2-R52CLowLikelyLikely pathogenic

Recessive, Carrier (Heterozygous)
0.048615This variant is associated with mannose binding protein deficiency which leads to impaired complement system immune response to mannose-rich pathogens. Patients homozygous for this allele or compound heterozygous are likely to have increased susceptibility to infection, but Hellemann et al. report heterosis for intensive care outcomes in heterozygous subjects. The wild-type version of this gene is known as variant allele A, while this is called variant allele D. See G54D (variant B) and G57E (variant C).1
5RNASEL-R462QLowUncertainUncertain pathogenic

Complex/Other, Heterozygous
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
6TGIF1-P83ShiftLowUncertainUncertain pathogenic

Complex/Other, Homozygous
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
7ELAC2-S217LLowUncertainUncertain pathogenic

Complex/Other, Homozygous
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
8KDR-C482RLowUncertainUncertain pathogenic

Complex/Other, Heterozygous
0.0209147Hypothesized to cause a higher risk of benign neonatal hemangiomas (which are seen in 10% of children). However, observations lacked statistical significance.1
9ACAD8-S171CLowUncertainUncertain pathogenic

Recessive, Carrier (Heterozygous)
0.018312This variant (a.k.a S149C) was found as a compound heterozygote (with M130T) in a male newborn of European descent with isobutyryl-CoA dehydrogenase deficiency (identified by newborn screening). Lack of controls means that significance cannot be established and allele frequency cannot be estimated. Oglesbee et al. comment that IBD-deficiency may be relatively benign, most cases identified by newborn screening have remained asymptomatic, but Ferreira et al. report a symptomatic individual homozygous for this variant.1
10HFE-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
11TP53-P72RLowUncertainUncertain pathogenic

Unknown, Heterozygous
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
12WFS1-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
13ELAC2-A541TLowUncertainUncertain pathogenic

Unknown, Heterozygous
0.0276074This variant is implicated as causing increased susceptibility to prostate cancer. However the variant has always been seen paired with S217L, it is unclear which variant is causal. Evidence is weak for both; one meta-analysis (Severi et al.) concluded that neither variant was pathogenic, a more recent meta-analysis (Xu et al.) found the data to be significant but the odds ratio was not strong and concluded they are "low-penetrance susceptibility markers of prostate cancer".1
14ERCC6-R1213GLowUncertainUncertain pathogenic

Recessive, Carrier (Heterozygous)
0.196877When homozygous, this variant may cause Cockayne Syndrome, which is a severe autosomal-recessive disorder characterized by abnormal early growth and development, abnormal sensitivity to sunlight, and premature aging. Cockayne Syndrome Type I and Type II lead to death in early childhood. Several other variants in the ERCC6 gene are linked to Cockayne Syndrome. This variant may also be linked to age-related macular degeneration like other ERCC6 variants, and has been linked to colorectal cancer in one study. 1
15SP110-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
16DPYD-M166VHighLikelyLikely pharmacogenetic

Unknown, Heterozygous
0.0778955Associated with DPYD deficiency and poor prognosis for chemotherapy w/ 5-flurorouracil. 1
17FUT2-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
18PRNP-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
19CASP10-V410ILowLikelyLikely protective

Dominant, Heterozygous
0.0474066Reported to have a protective effect on breast cancer. If the lifetime risk of breast cancer is 12%, women with this variant may have a lower risk of 8-9% (30% less than average).1
20NPC1-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
21KCNJ11-K23ELowLikelyLikely protective

Unknown, Heterozygous
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
22TOR1A-D216HLowLikelyLikely protective

Unknown, Heterozygous
0.102993This SNP has been shown to be benign and play a protective role against Dystonia. 1
23MTR-D919GLowUncertainUncertain protective

Complex/Other, Heterozygous
0.217234This variant was weakly associated with a protective effect vs. colorectal cancer, but only in individuals with low alcohol consumption. 1
24TYR-R402QLowWell-establishedWell-established benign

Complex/Other, Heterozygous
0.204964This is a frequent pigmentation polymorphism in Europeans that affects function of the Tyrosinase gene. It is associated with blue instead of green eyes and sun sensitivity. For the most part this variant is benign, but many individuals with ocular albinism (which affects only the eyes) carry this variant along with another more severe variant in the same gene.1
25PKD1-A4059VLowLikelyLikely benign

Unknown, Heterozygous
0.0570413Probably benign.1
26MSH2-G322DLowLikelyLikely benign

Unknown, Heterozygous
0.0110615Although other variants in this mismatch repair gene are associated with cancer, most publications dismiss this variant as a polymorphism (HapMap allele frequency of 1.6%).1
27NOTCH3-H1133QLowUncertainUncertain benign

Unknown, Heterozygous
0.0131995Probably benign.1
28BRCA1-Q356RLowUncertainUncertain benign

Unknown, Heterozygous
0.0462911One common variant associated this variant with an increased risk of breast cancer, but a more recent, larger study found no association.1
29POLG2-G416ALowUncertainUncertain benign

Unknown, Heterozygous
0.0119025Rare but presumed benign. It was believed to be non-causal in a patient with a different mutation, and functional analysis found no difference from wild type.1
30APOB-Y1422CLowUncertainUncertain benign

Unknown, Homozygous
0.999628This position is almost certainly an error in the HG18 reference sequence. 1
31PCSK9-G670ELowUncertainUncertain benign

Unknown, Homozygous
0.888269This variant is likely benign. 1
32TPCN2-G734ELowUncertainUncertain benign

Unknown, Heterozygous
0.286166Pigmentation allele.1
33TAS2R38-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
34RP1-N985YLowUncertainUncertain benign

Unknown, Heterozygous
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
35TAS2R38-A49PLowUncertainUncertain benign

Unknown, Heterozygous
0.431121This variant is strongly associated with causing the "taster" phenotype of phenylthiocarbamine (PTC) in a dominant manner.1
36RAPSN-R58CLowUncertainUncertain benign

Unknown, Heterozygous
0.0778026Reported as non-pathogenic polymorphism. 1
37PKP2-L366PLowUncertainUncertain benign

Unknown, Heterozygous
0.221231This variant is a benign polymorphism. 1
38SLC45A2-L374FLowUncertainUncertain benign

Unknown, Homozygous
0.691764Pigmentation allele for non-black hair, and consequently, possible increased susceptibility to malignant melanoma.1
VariantPrioritization scoreAllele
freq
Num of
articles
Zygosity and Prioritization Score Reasons

Gene search

"GENE" or "GENE A123C":

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