SSR4 p.Ser91=
c.273C>T · VCV4953362
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000112%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.127 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP 0.69, phastCons 1 |
| Overall | ||
| CADD | 7.636 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000112%
European (non-Finnish) · 1/894,908 alleles
Overall
9.12e-05%
1/1,096,819 alleles · very rare
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.Ser91=
- Coding
- c.273C>T
- MANE Select
- NM_006280
- Type
- single nucleotide variant
- Location
- chrX:153797736 (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-ser91 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown