OGT p.Val505=
c.1515G>A · rs34739713 · VCV1233568
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 14.1%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.3 | GERP -3.9, phastCons 1 |
| Overall | ||
| CADD | 7.493 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
14.1%
African / African-American · 8,035/57,122 alleles
Filtering AF
13.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 13.7%
Overall
0.749%
9,046/1,208,010 alleles · common
exomes 4,641/1,096,020 · genomes 4,405/111,990 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 14.1% | 7 |
| Remaining individualsnot grpmax-eligible | 0.957% | 105 |
| Admixed American | 0.906% | 110 |
| Middle Eastern | 0.369% | 271 |
| South Asian | 0.0335% | 2,987 |
| European (non-Finnish) | 0.012% | 8,350 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- OGT
- Protein
- p.Val505=
- Coding
- c.1515G>A
- MANE Select
- NM_181672
- dbSNP
- rs34739713
- Type
- single nucleotide variant
- Location
- chrX:71557585 (GRCh38)
- Structure
- AlphaFold pLDDT 93.41 · 44 PDB
Similar variants
- OGT p.Thr932Ile Likely pathogenic ★★ same type
- OGT p.Ala765Thr Uncertain significance ★★ ⚠ same type
- OGT p.Arg117Cys Uncertain significance ★★ same type
- OGT p.Arg485Gln Uncertain significance ★★ ⚠ same type
- OGT p.Arg555Trp Uncertain significance ★★ ⚠ same type
- OGT p.Arg627Cys Uncertain significance ★★ ⚠ same type
- OGT p.Arg899His Uncertain significance ★★ ⚠ same type
- OGT p.Asn898Ser Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ogt-p-val505 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown