SDHAF2 p.Pro51=
c.153T>A · rs769950627 · VCV2030937
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
hereditary pheochromocytoma-paraganglioma
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.082 | GERP -1.1, phastCons 0.83 |
| Overall | ||
| CADD | 12.32 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- SDHAF2
- Protein
- p.Pro51=
- Coding
- c.153T>A
- MANE Select
- NM_017841
- dbSNP
- rs769950627
- Type
- single nucleotide variant
- Location
- chr11:61437741 (GRCh38)
- Gene constraint
- LOEUF 1.608 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 84.06 · 2 PDB
- Residue 51
- an α-helix
Disease context
hereditary pheochromocytoma-paraganglioma — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Hereditary pheochromocytoma-paraganglioma (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- Childhood
- Prevalence
- 1-9 / 1 000 000 (Worldwide)
Similar variants
- SDHAF2 p.Pro51Arg Uncertain significance ★★ ⚠ same residue
- SDHAF2 p.Pro51Leu Uncertain significance ★★ ⚠ same residue
- SDHAF2 p.Pro51Ser 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
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-pro51 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown