OGT p.Ser693=
c.2079C>T · rs770630335 · VCV2981214
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.023%, mid)
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 -0.21 | GERP -0.64, phastCons 0.58 |
| Overall | ||
| CADD | 5.903 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.023%
Middle Eastern · 1/4,355 alleles
Filtering AF
0.00236%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00125%
Overall
0.00166%
20/1,207,989 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.023% | 4,355 |
| East Asian | 0.00889% | 11,242 |
| South Asian | 0.00529% | 18,893 |
| Admixed American | 0.00219% | 45,559 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,560 |
| European (non-Finnish) | 0.00123% | 81,278 |
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.Ser693=
- Coding
- c.2079C>T
- MANE Select
- NM_181672
- dbSNP
- rs770630335
- Type
- single nucleotide variant
- Location
- chrX:71562948 (GRCh38)
- Structure
- AlphaFold pLDDT 93.41 · 44 PDB
- Residue 693
- a β-strand
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-ser693 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown