GLS p.Pro313=
c.939G>A · rs75276497 · VCV3025273
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.147%, eas)
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 -0.48 | GERP -4.7 |
| Overall | ||
| CADD | 8.334 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.147%
East Asian · 66/44,786 alleles
Filtering AF
0.119%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.108%
Overall
0.0114%
183/1,605,934 alleles · rare
exomes 164/1,453,738 · genomes 19/152,196 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.147% | 679 |
| Middle Eastern | 0.0496% | 2,015 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0373% | 2,683 |
| Remaining individualsnot grpmax-eligible | 0.0209% | 4,788 |
| South Asian | 0.0188% | 5,332 |
| European (non-Finnish) | 0.00605% | 16,527 |
| African / African-American | 0.00267% | 37,409 |
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
- GLS
- Protein
- p.Pro313=
- Coding
- c.939G>A
- MANE Select
- NM_014905
- dbSNP
- rs75276497
- Type
- single nucleotide variant
- Location
- chr2:190905127 (GRCh38)
- Structure
- AlphaFold pLDDT 85.66 · 4 PDB
- Residue 313
- an α-helix
Similar variants
- GLS p.Pro313Leu Pathogenic same residue
- GLS p.Ala99Thr Uncertain significance ★★ ⚠ same type
- GLS p.Leu25Arg Uncertain significance ★★ ⚠ same type
- GLS c.387-3T>C Likely benign ★★ same type
- GLS p.Ala561= Benign ★★ same type
- GLS p.Arg53= Likely benign ★★ same type
- GLS p.Val554= Likely benign ★★ same type
- GLS2 p.Gly337= Benign ★★ 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/gls-p-pro313 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown