OGT p.Ala952=
c.2856T>C · rs200283810 · VCV2718903
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0911%, amr)
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 1.1 | GERP 0.54, phastCons 1 |
| Overall | ||
| CADD | 12.22 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0911%
Admixed American · 41/45,003 alleles
Filtering AF
0.069%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0612%
Overall
0.0048%
58/1,207,417 alleles · ultra-rare
exomes 24/1,094,654 · genomes 34/112,763 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0911% | 1,098 |
| Remaining individualsnot grpmax-eligible | 0.0295% | 3,392 |
| European (non-Finnish) | 0.000335% | 298,100 |
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.Ala952=
- Coding
- c.2856T>C
- MANE Select
- NM_181672
- dbSNP
- rs200283810
- Type
- single nucleotide variant
- Location
- chrX:71568006 (GRCh38)
- Structure
- AlphaFold pLDDT 93.41 · 44 PDB
- Residue 952
- an α-helix
Similar variants
- OGT p.Ala952Val Uncertain significance ★ ⚠ same residue
- 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
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-ala952 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown