SDHD p.Ala9=
c.27C>A · rs1555186670 · VCV465231
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Conditions
3
pheochromocytoma
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 -0.77 | GERP -3.1 |
| Overall | ||
| CADD | 6.729 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,028 alleles
Overall
6.2e-05%
1/1,614,172 alleles · very rare
exomes 1/1,461,886 · genomes 0/152,286 · 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
- SDHD
- Protein
- p.Ala9=
- Coding
- c.27C>A
- MANE Select
- NM_003002
- dbSNP
- rs1555186670
- Type
- single nucleotide variant
- Location
- chr11:112086934 (GRCh38)
- Gene constraint
- LOEUF 0.581 · pLI 0.91 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 81.50 · 2 PDB
Similar variants
- SDHD p.Ala9Ser Uncertain significance ★★ ⚠ same residue
- SDHD c.170-1G>T Pathogenic ★★ same condition
- SDHD c.170-2A>G Pathogenic/Likely pathogenic ★★ same condition
- SDHD c.314+1G>A Pathogenic ★★ same condition
- SDHD c.314+1G>T Pathogenic ★★ same condition
- SDHD c.315-1G>A Likely pathogenic ★★ same condition
- SDHD c.315-2A>T Pathogenic/Likely pathogenic ★★ same condition
- SDHD p.Arg22Ter 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/sdhd-p-ala9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown