Is SDHA p.Ala660= (c.1980C>G) pathogenic?

SDHA p.Ala660= (c.1980C>G) is classified Likely benign in SDHA (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-09). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with SDHA p.Ala660= (c.1980C>G)?

SDHA p.Ala660= (c.1980C>G) is associated with hereditary neoplastic syndrome (ClinVar).

How common is SDHA p.Ala660= (c.1980C>G) in the general population?

SDHA p.Ala660= (c.1980C>G) is absent from gnomAD v4.1 (gnomAD).

SDHA p.Ala660=

c.1980C>G · rs2477489680 · VCV2587087

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

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 0.34	GERP -3.4, phastCons 0.99
Overall
CADD	4.422	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: SDHA
Protein: p.Ala660=
Coding: c.1980C>G
MANE Select: NM_004168
dbSNP: rs2477489680
Type: single nucleotide variant
Location: chr5:256405 (GRCh38)
Gene constraint: LOEUF 0.786 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.06 · 5 PDB

Full SDHA gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SDHA p.Ala660Thr Uncertain significance ★★ ⚠ same residue
SDHA p.Ala660Val Uncertain significance ★★ ⚠ same residue
SDHA p.Ala660Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
SDHA c.1064+1G>T Likely pathogenic ★★ same condition
SDHA c.1064+2T>A Likely pathogenic ★★ same condition
SDHA c.1261-1G>A Likely pathogenic ★★ same condition
SDHA c.1261-2A>G Likely pathogenic ★★ same condition
SDHA c.151-1G>C 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/sdha-p-ala660 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown