Is SDHA p.Phe62fs (c.186del) pathogenic?

SDHA p.Phe62fs (c.186del) is classified Pathogenic in SDHA (ClinVar, Single submitter, 1 submitter; last evaluated 2020-02-18). No gnomAD frequency available for this variant; Associated with hereditary neoplastic syndrome.

What condition is associated with SDHA p.Phe62fs (c.186del)?

SDHA p.Phe62fs (c.186del) is associated with hereditary neoplastic syndrome (ClinVar).

How common is SDHA p.Phe62fs (c.186del) in the general population?

SDHA p.Phe62fs (c.186del) is no gnomAD frequency available for this variant (gnomAD).

SDHA p.Phe62fs

c.186del · rs2477285645 · VCV1781657

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 3 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.1	GERP -0.3, phastCons 1
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: SDHA
Protein: p.Phe62fs
Coding: c.186del
MANE Select: NM_004168
dbSNP: rs2477285645
Type: Deletion
Location: chr5:224393 (GRCh38)
Gene constraint: LOEUF 0.786 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.06 · 5 PDB
Residue 62: a β-strand

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.Phe62Val Uncertain significance ★ ⚠ same residue
SDHA p.Phe62= Likely benign ★ same residue
SDHA c.1432_1432+1del Pathogenic/Likely pathogenic ★★ same condition
SDHA c.457-2_457del Pathogenic/Likely pathogenic ★★ same condition
SDHA c.63+2del Likely pathogenic ★★ same condition
SDHA c.762_770+17del Pathogenic/Likely pathogenic ★★ same condition
SDHA p.Ala338fs Pathogenic ★★ same condition
SDHA p.Arg162fs 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/sdha-p-phe62fs (accessed [today's date]).

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