OGT p.Phe651=
c.1953T>C · rs370997825 · VCV2883356
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.107%, afr)
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 0.89 | GERP 0.69, phastCons 1 |
| Overall | ||
| CADD | 9.361 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.107%
African / African-American · 61/57,038 alleles
Filtering AF
0.0854%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0776%
Overall
0.00573%
69/1,204,468 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.107% | 935 |
| Admixed American | 0.00894% | 11,186 |
| Remaining individualsnot grpmax-eligible | 0.00633% | 15,786 |
| European (non-Finnish) | 0.000112% | 892,977 |
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.Phe651=
- Coding
- c.1953T>C
- MANE Select
- NM_181672
- dbSNP
- rs370997825
- Type
- single nucleotide variant
- Location
- chrX:71561876 (GRCh38)
- Structure
- AlphaFold pLDDT 93.41 · 44 PDB
- Residue 651
- an α-helix
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-phe651 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown