OGT p.His930=
c.2790C>T · VCV4747620
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0157%, 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 -2.6 | GERP -2.8 |
| Overall | ||
| CADD | 5.946 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0157%
African / African-American · 9/57,310 alleles
Filtering AF
0.00816%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00602%
Overall
0.000912%
11/1,206,505 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0157% | 6,368 |
| Remaining individualsnot grpmax-eligible | 0.00421% | 23,732 |
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.His930=
- Coding
- c.2790C>T
- MANE Select
- NM_181672
- Type
- single nucleotide variant
- Location
- chrX:71567700 (GRCh38)
- Structure
- AlphaFold pLDDT 93.41 · 44 PDB
- Residue 930
- a binding site
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-his930 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown