Is COA7 p.Asp33fs (c.97del) pathogenic?

COA7 p.Asp33fs (c.97del) is classified Likely pathogenic in COA7 (ClinVar, Single submitter, 1 submitter). Very rare (popmax 0.0011%, sas); Associated with spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 3.

What condition is associated with COA7 p.Asp33fs (c.97del)?

COA7 p.Asp33fs (c.97del) is associated with spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 3 (ClinVar).

How common is COA7 p.Asp33fs (c.97del) in the general population?

COA7 p.Asp33fs (c.97del) is very rare (popmax 0.0011%, sas) (gnomAD).

COA7 p.Asp33fs

c.97del · rs767873164 · VCV2585171

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

Conditions

spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 3

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 1 of 3
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	phastCons 1

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/90,980 alleles

Overall 6.21e-05% 1/1,610,160 alleles · very rare exomes 1/1,457,970 · genomes 0/152,190 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: COA7
Protein: p.Asp33fs
Coding: c.97del
MANE Select: NM_023077
dbSNP: rs767873164
Type: Deletion
Location: chr1:52698230 (GRCh38)
Gene constraint: LOEUF 0.867 · pLI 0.04 (gnomAD)
Structure: AlphaFold pLDDT 95.47 · 1 PDB

Full COA7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

COA7 p.Gly144fs Pathogenic same condition
COA7 p.Tyr38Cys Uncertain significance ★★ ⚠ same condition
COA7 c.247+1G>T Pathogenic same condition
COA7 p.Asp6Gly Pathogenic ⚠ same condition
COA7 p.Ser149Ile Pathogenic same condition
COA7 p.Tyr137Cys 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/coa7-p-asp33fs (accessed [today's date]).

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