Is SDHA p.Pro359fs (c.1075_1078del) pathogenic?

SDHA p.Pro359fs (c.10751078del) is classified Pathogenic in SDHA (ClinVar, Single submitter, 1 submitter; last evaluated 2020-09-04). No gnomAD frequency available for this variant.

How common is SDHA p.Pro359fs (c.1075_1078del) in the general population?

SDHA p.Pro359fs (c.1075_1078del) is no gnomAD frequency available for this variant (gnomAD).

SDHA p.Pro359fs

c.1075_1078del · rs2126584181 · VCV1323568

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

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 9 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.31	GERP -3.5, phastCons 0.12
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.Pro359fs
Coding: c.1075_1078del
MANE Select: NM_004168
dbSNP: rs2126584181
Type: Deletion
Location: chr5:235154 (GRCh38)
Gene constraint: LOEUF 0.786 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.06 · 5 PDB
Residue 359: a turn

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

Similar variants

SDHA p.Pro359Arg Uncertain significance ★ ⚠ same residue
SDHA p.Pro359Leu Uncertain significance ★ ⚠ same residue
SDHA p.Pro359Ser Uncertain significance ★ ⚠ same residue
SDHA c.1432_1432+1del Pathogenic/Likely pathogenic ★★ same type
SDHA c.457-2_457del Pathogenic/Likely pathogenic ★★ same type
SDHA c.63+2del Likely pathogenic ★★ same type
SDHA c.762_770+17del Pathogenic/Likely pathogenic ★★ same type
SDHA c.895+1del Likely pathogenic ★★ same type

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-pro359fs (accessed [today's date]).

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