SOX5 p.Val271=
c.813T>C · VCV4075273
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0234%, amr)
Conditions
1
congenital anomaly of kidney and urinary tract
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 2.7 | GERP -0.069, phastCons 1 |
| Overall | ||
| CADD | 9.767 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0234%
Admixed American · 14/59,806 alleles
Filtering AF
0.0141%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0113%
Overall
0.00664%
107/1,612,146 alleles · ultra-rare
exomes 101/1,459,982 · genomes 6/152,164 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0234% | 4,272 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0102% | 9,824 |
| European (non-Finnish) | 0.00746% | 13,398 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,196 |
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
- SOX5
- Protein
- p.Val271=
- Coding
- c.813T>C
- MANE Select
- NM_006940
- Type
- single nucleotide variant
- Location
- chr12:23665562 (GRCh38)
- Gene constraint
- LOEUF 0.204 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.95
Similar variants
- SOX5 c.1164+2T>G Pathogenic ★★ same type
- SOX5 p.Arg118Ter Pathogenic ★★ same type
- SOX5 p.Arg213Ter Pathogenic/Likely pathogenic ★★ same type
- SOX5 p.Arg471Ter Pathogenic/Likely pathogenic ★★ same type
- SOX5 p.Arg493Ter Pathogenic ★★ same type
- SOX5 p.Arg558Cys Pathogenic/Likely pathogenic ★★ same type
- SOX5 p.Arg558His Pathogenic/Likely pathogenic ★★ same type
- SOX5 p.Arg571Gln Pathogenic/Likely pathogenic ★★ 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/sox5-p-val271 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown