SSR4 p.Pro129=
c.387G>A · rs782786758 · VCV2201570
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0575%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.008 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.27 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP -2.3 | GERP -3.7 |
| Overall | ||
| CADD | 0.116 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0575%
East Asian · 16/27,850 alleles
Filtering AF
0.036%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0293%
Overall
0.00202%
23/1,137,955 alleles · ultra-rare
exomes 23/1,034,482 · genomes 0/103,473 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0575% | 1,741 |
| South Asian | 0.00358% | 27,908 |
| Remaining individualsnot grpmax-eligible | 0.00232% | 43,044 |
| European (non-Finnish) | 0.00047% | 212,964 |
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
- SSR4
- Protein
- p.Pro129=
- Coding
- c.387G>A
- MANE Select
- NM_006280
- dbSNP
- rs782786758
- Type
- single nucleotide variant
- Location
- chrX:153798106 (GRCh38)
- Structure
- AlphaFold pLDDT 89.09 · 3 PDB
Similar variants
- SSR4 p.Ala11Val Uncertain significance ★★ ⚠ same type
- SSR4 p.Ala154Val Uncertain significance ★★ ⚠ same type
- SSR4 p.Ala97Thr Uncertain significance ★★ ⚠ same type
- SSR4 p.Arg105Lys Uncertain significance ★★ ⚠ same type
- SSR4 p.Ile43Val Uncertain significance ★★ ⚠ same type
- SSR4 p.Ser166Gly Uncertain significance ★★ ⚠ same type
- SSR4 p.Thr141Ala Uncertain significance ★★ ⚠ same type
- SSR4 p.Val48Ile 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/ssr4-p-pro129 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown