SDHAF2 p.Val136=
c.408C>A · rs2540133031 · VCV2448517
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
Conditions
1
hereditary neoplastic syndrome
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 1.4 | GERP 2.1, phastCons 0.9 |
| Overall | ||
| CADD | 8.928 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,066 alleles
Overall
6.2e-05%
1/1,614,168 alleles · very rare
exomes 1/1,461,848 · genomes 0/152,320 · joint denominator
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
- SDHAF2
- Protein
- p.Val136=
- Coding
- c.408C>A
- MANE Select
- NM_017841
- dbSNP
- rs2540133031
- Type
- single nucleotide variant
- Location
- chr11:61445978 (GRCh38)
- Gene constraint
- LOEUF 1.608 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 84.06 · 2 PDB
- Residue 136
- an α-helix
Similar variants
- SDHAF2 p.Val136Ala Uncertain significance ★ ⚠ same residue
- SDHAF2 p.Val136Ile Uncertain significance ★ ⚠ same residue
- SDHAF2 c.260+1G>A Likely pathogenic ★★ same condition
- SDHAF2 c.261-2A>G Likely pathogenic ★★ same condition
- SDHAF2 c.261-2A>T Likely pathogenic ★★ same condition
- SDHAF2 c.37-1G>C Pathogenic/Likely pathogenic ★★ same condition
- SDHAF2 c.37-2A>G Pathogenic/Likely pathogenic ★★ same condition
- SDHAF2 c.370+1G>T Likely pathogenic ★★ same condition
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/sdhaf2-p-val136 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown