SDHD p.Ser59fs
c.174del · VCV4786820
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
3
pheochromocytoma
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 3 of 4 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP -2, phastCons 0.97 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- SDHD
- Protein
- p.Ser59fs
- Coding
- c.174del
- MANE Select
- NM_003002
- Type
- Deletion
- Location
- chr11:112088871 (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.Ser59Phe Uncertain significance ★★ ⚠ same residue
- SDHD p.Ser59Pro Uncertain significance ★★ ⚠ same residue
- SDHD p.Ser59= Benign/Likely benign ★★ same residue
- SDHD p.Gln109fs Pathogenic ★★ same condition
- SDHD p.Gly58fs Pathogenic ★★ same condition
- SDHD p.Leu128fs Pathogenic ★★ same condition
- SDHD p.Leu20fs Pathogenic ★★ same condition
- SDHD p.Pro81fs 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-ser59fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown