Is SDHD p.Ala62= (c.186A>T) pathogenic?

SDHD p.Ala62= (c.186A>T) is classified Likely benign in SDHD (ClinVar, Single submitter, 1 submitter; last evaluated 2019-02-10). Absent from gnomAD v4.1; Associated with Paragangliomas with sensorineural hearing loss.

What condition is associated with SDHD p.Ala62= (c.186A>T)?

SDHD p.Ala62= (c.186A>T) is associated with Paragangliomas with sensorineural hearing loss, pheochromocytoma, Carney-Stratakis syndrome (ClinVar).

How common is SDHD p.Ala62= (c.186A>T) in the general population?

SDHD p.Ala62= (c.186A>T) is absent from gnomAD v4.1 (gnomAD).

SDHD p.Ala62=

c.186A>T · rs11547899 · VCV1089817

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Paragangliomas with sensorineural hearing loss

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 -3.2	GERP -4.3
Overall
CADD	0.838	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: SDHD
Protein: p.Ala62=
Coding: c.186A>T
MANE Select: NM_003002
dbSNP: rs11547899
Type: single nucleotide variant
Location: chr11:112088883 (GRCh38)
Gene constraint: LOEUF 0.581 · pLI 0.91 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 81.50 · 2 PDB

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

Disease context

Paragangliomas with sensorineural hearing loss — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: pheochromocytoma Carney-Stratakis syndrome Cowden syndrome 3

Similar variants

SDHD p.Ala62Val 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-ala62 (accessed [today's date]).

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