hu689E16 (Ale A) - GET-Evidence variant report

Variant report for hu689E16 (Ale A)

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VariantClinical
Importance
ImpactAllele
freq
Summary
1UGT1A1-G71RModerateLikelyLikely pathogenic

Complex/Other, Heterozygous
0.000743632This variant, also known as UGT1A1*6, is associated with Gilbert syndrome (found in ~5% of the population) and transient hyperbilirubinemia in infants in east asian populations. This allele appears to have incomplete penetrance and causes reduced enzyme activity.1
2GJB2-V37IModerateLikelyLikely pathogenic

Recessive, Carrier (Heterozygous)
0.00148726This recessive variant is associated with mild hearing loss in Asians.1
3MEFV-E148QModerateUncertainUncertain pathogenic

Recessive, Carrier (Heterozygous)
0.0120929Some reports believe this cause Familial Mediterranean Fever in a recessive manner with reduced penetrance (i.e. not all get the disease). However, these reports lack strong statistical significance; other studies argue the variant is not associated with the disease.1
4COL4A1-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
5WFS1-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
6RNASEL-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
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
8H6PD-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
9TP53-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
10BRCA2-N372HLowUncertainUncertain pathogenic

Recessive, Carrier (Heterozygous)
0.23656This is a common variant of BRCA2 (HapMap allele frequency of 23%). The variant is weakly associated with an increased chance of breast cancer, and zygosity of the variant is associated with sex of children: male children are more likely to be homozygous for this variant, female children are more likely to be heterozygous.1
11TPMT-Y240CLowWell-establishedWell-established pharmacogenetic

Complex/Other, Heterozygous
0.0461825Alone, this variant is known as TPMT*3C -- but often, especially in Caucasians, it is found together with another nonsynonymous variant (A154T) to produce the TPMT*3A variant. Both variants are associated with loss of thiopurine methyltransferase (TPMT) activity, although *3C is milder than *3A. Inability to metabolize thiopurine drugs can lead to severe adverse reactions. Heterozygotes may be advised to take a reduced dosage due to reduced metabolism of the drug.1
12rs1544410LowUncertainUncertain 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
13CFH-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
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
15TOR1A-D216HLowLikelyLikely protective

Unknown, Heterozygous
0.102993This SNP has been shown to be benign and play a protective role against Dystonia. 1
16IL7R-T244ILowLikelyLikely protective

Unknown, Heterozygous
0.210169The reference genome variant for this allele has been associated with a slight increased risk of multiple sclerosis. Thus, this variant can be treated as a "protective" variant -- carriers of this variant are slightly less likely to have MS. Because the disease is rare and the effect of this variant is not very strong, the absolute decreased risk for carriers of this variant is less than .05% (less than 1 in 2000).1
17KCNJ11-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
18ARSA-N350SLowWell-establishedWell-established benign

Unknown, Heterozygous
0.183199This common variant (HapMap 24.1% allele frequency) causes a loss of a glycosylation site (affecting the size of the protein when studied with gel electrophoresis) but does not affect enzyme activity or stability.1
19OCA2-H615RLowLikelyLikely benign

Complex/Other, Homozygous
0.000650678Associated with lighter skin pigmentation in East Asian populations.1
20SLC45A2-E272KLowLikelyLikely benign

Unknown, Heterozygous
0.0290946Pigmentation allele for black hair in Caucasian population.1
21LOXL1-R141LLowUncertainUncertain benign

Complex/Other, Heterozygous
0.255899Associated with exfoliative glaucoma & syndrome (XFG & XFS) in various populations, but with contradicting results (protective in Caucasians, pathogenic in Japanese). Based on this it seems the variation itself -- although it affects protein structure -- is not itself causing disease. Instead it is likely associated with other nearby causal variants. As such, it is evaluated as benign by GET-Evidence (which focuses on reporting causal variants). See detailed variant report for disease risk associations.1
22EDAR-V370ALowUncertainUncertain benign

Unknown, Homozygous
0.0105968Associated with thicker hair, common in Chinese and Japanese individuals and thought to be Asian-specific.1
23ABCC11-G180RLowUncertainUncertain benign

Unknown, Heterozygous
0.0976947This variant is associated with dry type ear wax (a benign trait) in a recessive manner.1
24PTCH1-P1315LLowUncertainUncertain benign

Unknown, Heterozygous
0.29631Common polymorphism, presumed benign.1
25TAS2R38-A49PLowUncertainUncertain benign

Unknown, Heterozygous
0.431121This variant is strongly associated with causing the "taster" phenotype of phenylthiocarbamine (PTC) in a dominant manner.1
26TAS2R38-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
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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