Variant report for hu7EB316
- Data source: CGI sample GS02269-DNA_A03 from PGP sample
- This report: evidence.pgp-hms.org/genomes?display_genome_id=a04d80aadc25cd6395ef62efc5483f862e7e4974&access_token=6d662e7858a96af1ea2e388f13ec616b
- Person ID: hu7EB316
- public profile: my.pgp-hms.org/profile/hu7EB316
- Download: source data
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Log file:
| Row number | Variant | Clinical Importance | Evidence | Impact | Allele freq | Summary | Sufficient |
|---|---|---|---|---|---|---|---|
| 1 | FLG-S761Shift | Moderate | Uncertain | Uncertain pathogenic Complex/Other, Heterozygous | 0.00793651 | Based on other severe variants in the same gene, this variant is likely to cause ichthyosis vulgaris when homozygous or compound heterozygous with another severe variant. Some authors report the variant has incomplete dominance, with heterozygotes generally having a very mild phenotype: some palmar hyperlinearity, keratosis pilaris and, in some cases fine scale. | 1 |
| 2 | COL4A1-Q1334H | Low | Likely | Likely pathogenic Dominant, Heterozygous | 0.324689 | This 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 |
| 3 | MTRR-I49M | Low | Likely | Likely pathogenic Recessive, Carrier (Heterozygous) | 0.451199 | This 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 |
| 4 | CETP-A390P | Low | Likely | Likely pathogenic Unknown, Heterozygous | 0.0388548 | This variant is associated with slightly lower HDL (good) cholesterol, although it has a negligible effect (around 2 mg/dl). | 1 |
| 5 | PRF1-R4H | Low | Uncertain | Uncertain pathogenic Dominant, Heterozygous | 0.0272881 | This rare variant was reported seen in an individual with acquired aplastic anemia, but the frequency of this allele in controls indicates is no different from the cases, indicating this is likely a polymorphism without dramatic functional effect. | 1 |
| 6 | ELAC2-S217L | Low | Uncertain | Uncertain pathogenic Complex/Other, Heterozygous | 0.273471 | Reported 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 |
| 7 | ERCC6-R1213G | Low | Uncertain | Uncertain pathogenic Recessive, Carrier (Heterozygous) | 0.196877 | When 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 |
| 8 | SP110-L425S | Low | Uncertain | Uncertain pathogenic Unknown, Homozygous | 0.863357 | This 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 |
| 9 | DYX1C1-E417X | Low | Uncertain | Uncertain pathogenic Unknown, Heterozygous | 0.20147 | One study reports this variant to be associated with dyslexia. The study group was relatively small and so the results did not have strong significance. If they are representative this variant is associated with a doubled risk for dyslexia, but it is unclear whether the effect would be additive, dominant, or recessive. | 1 |
| 10 | HFE-H63D | Low | Uncertain | Uncertain pathogenic Recessive, Carrier (Heterozygous) | 0.109965 | There 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 |
| 11 | TP53-P72R | Low | Uncertain | Uncertain pathogenic Unknown, Homozygous | 0.627743 | This 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 |
| 12 | ITPA-P32T | Low | Well-established | Well-established pharmacogenetic Recessive, Carrier (Heterozygous) | 0.0609779 | This variant is associated with inosine triphosphate pyrophosphohydrolase deficiency and may be associated with an adverse reaction to thiopurine drugs (which are used as immunosuppressants). Homozygotes have no detectable ITPase activity, individuals compound heterozygous with another less severe mutation also have severely reduced enzyme activity. | 1 |
| 13 | rs1544410 | Low | Uncertain | Uncertain pharmacogenetic Unknown, Heterozygous | 0.351562 | rs1544410 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 |
| 14 | ABCC6-R1268Q | Low | Uncertain | Uncertain pharmacogenetic Unknown, Heterozygous | 0.218907 | This 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 |
| 15 | KCNJ11-K23E | Low | Likely | Likely protective Unknown, Homozygous | 0.738148 | This 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 |
| 16 | MTR-D919G | Low | Uncertain | Uncertain protective Complex/Other, Heterozygous | 0.217234 | This variant was weakly associated with a protective effect vs. colorectal cancer, but only in individuals with low alcohol consumption. | 1 |
| 17 | IRS2-G1057D | Low | Uncertain | Uncertain protective Unknown, Heterozygous | 0.232615 | a.k.a Gly1057Asp, insulin receptor substrate-2 IRS2. The rs1805097(G) allele is associated with the Gly, and the (A) allele with Asp. A longevity study concluded that rs1805097(A;A) individuals were about twice as likely to live over 85 y/o (odds ratio 2.03, CI:1.39-2.99, p = .0003). | 1 |
| 18 | ARSA-N350S | Low | Well-established | Well-established benign Unknown, Heterozygous | 0.183199 | This 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 |
| 19 | GABRD-R220H | Low | Likely | Likely benign Unknown, Heterozygous | 0.0161891 | Probably benign, one report hypothesized this variant was associated with epilepsy, but a follow-up investigation failed to establish any statistically significant difference for this variant's incidence in control vs. affected populations. | 1 |
| 20 | PMS2-P470S | Low | Likely | Likely benign Unknown, Heterozygous | 0.374884 | Benign, common variant. | 1 |
| 21 | RPGRIP1-A547S | Low | Uncertain | Uncertain benign Complex/Other, Heterozygous | 0.232202 | Probably benign. Implicated in causing autosomal recessive cone-rod dystrophy, but a later report found the same incidence in controls and concludes it is not causal. | 1 |
| 22 | TAS2R38-A49P | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 0.431121 | This variant is strongly associated with causing the "taster" phenotype of phenylthiocarbamine (PTC) in a dominant manner. | 1 |
| 23 | APOB-Y1422C | Low | Uncertain | Uncertain benign Unknown, Homozygous | 0.999628 | This position is almost certainly an error in the HG18 reference sequence. | 1 |
| 24 | TAS2R38-I296V | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 0.463376 | This 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 |
| 25 | DSPP-R68W | Low | Uncertain | Uncertain benign Unknown, Homozygous | 0.143045 | Probably 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 |
| 26 | SLC45A2-L374F | Low | Uncertain | Uncertain benign Unknown, Homozygous | 0.691764 | Pigmentation allele for non-black hair, and consequently, possible increased susceptibility to malignant melanoma. | 1 |
| 27 | PCSK9-G670E | Low | Uncertain | Uncertain benign Unknown, Homozygous | 0.888269 | This variant is likely benign. | 1 |
| 28 | PHYH-P29S | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 0.155326 | Probably benign. This variant was implicated as causing Refsum Disease in a recessive manner, but a subsequent publication noted that all instances were linked with other explanatory mutations. The high allele frequency of this variant in the population (7-13%) contradicts a pathogenic hypothesis. | 1 |
| 29 | PKP2-L366P | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 0.221231 | This variant is a benign polymorphism. | 1 |
| 30 | FMO3-V257M | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 0.0570738 | This common variant (HapMap allele frequency of 9.2%) appears to have no functional effect. OMIM has recorded it as having been seen homozygously in an individual with Trimethylaminuria, but Treacy et al. 1998 conclude it is a polymorphism. | 1 |
| 31 | FANCA-S1088F | Low | Uncertain | Uncertain benign Unknown, Heterozygous | 0.0584681 | Probably benign. One report hypothesized this variant causing Fanconi Anemia, but the allele frequency (3-7%) is high enough to contradict a highly penetrant pathogenic effect. Later authors have concluded this is a polymorphism, not pathogenic. | 1 |
| Row number | Variant | Prioritization score | Allele freq | Num of articles | Zygosity and Prioritization Score Reasons | Sufficient |
|---|