Is SDHA p.Phe173fs (c.514_517dup) pathogenic?

SDHA p.Phe173fs (c.514517dup) is classified Pathogenic in SDHA (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-10). No gnomAD frequency available for this variant; Associated with mitochondrial complex II deficiency, nuclear type 1.

What condition is associated with SDHA p.Phe173fs (c.514_517dup)?

SDHA p.Phe173fs (c.514_517dup) is associated with mitochondrial complex II deficiency, nuclear type 1, pheochromocytoma/paraganglioma syndrome 5 (ClinVar).

How common is SDHA p.Phe173fs (c.514_517dup) in the general population?

SDHA p.Phe173fs (c.514_517dup) is no gnomAD frequency available for this variant (gnomAD).

How is Isolated succinate-CoQ reductase deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

SDHA p.Phe173fs

c.514_517dup · rs2477299633 · VCV2951830

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

mitochondrial complex II deficiency, nuclear type 1

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 5 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.8	GERP 1.9, 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.Phe173fs
Coding: c.514_517dup
MANE Select: NM_004168
dbSNP: rs2477299633
Type: Duplication
Location: chr5:225938 (GRCh38)
Gene constraint: LOEUF 0.786 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.06 · 5 PDB
Residue 173: a β-strand

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

Disease context

mitochondrial complex II deficiency, nuclear type 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: pheochromocytoma/paraganglioma syndrome 5

For Isolated succinate-CoQ reductase deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

SDHA p.Ala102fs Pathogenic ★★ same condition
SDHA p.Ala186fs Pathogenic/Likely pathogenic ★★ same condition
SDHA p.Asn416fs Pathogenic ★★ same condition
SDHA p.Cys231fs Pathogenic ★★ same condition
SDHA p.Gly29fs Pathogenic ★★ same condition
SDHA p.Gly316fs Pathogenic/Likely pathogenic ★★ same condition
SDHA p.His34fs Pathogenic ★★ same condition
SDHA p.Ile539fs 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-phe173fs (accessed [today's date]).

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