Is COA5 p.Pro9= (c.27G>A) pathogenic?

COA5 p.Pro9= (c.27G>A) is classified Likely benign in COA5 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-15). No allele count reported in gnomAD v4.1 (AN 1,605,402).

How common is COA5 p.Pro9= (c.27G>A) in the general population?

COA5 p.Pro9= (c.27G>A) is no allele count reported in gnomAD v4.1 (AN 1,605,402) (gnomAD).

COA5 p.Pro9=

c.27G>A · VCV4716206

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,605,402)

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 -4.8	GERP -5.3
Overall
CADD	4.229	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,605,402). 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: COA5
Protein: p.Pro9=
Coding: c.27G>A
MANE Select: NM_001008215
Type: single nucleotide variant
Location: chr2:98608379 (GRCh38)
Gene constraint: LOEUF 1.852 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.42

Full COA5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

COA5 p.Pro9Leu Likely benign ★★ same residue
COA5 p.Ala53Thr Uncertain significance ★★ ⚠ same type
COA5 p.Ala66Val Uncertain significance ★★ ⚠ same type
COA5 c.100-239A>G Benign ★★ same type
COA5 c.100-53A>G Benign ★★ same type
COA5 c.99+28G>A Benign ★★ same type
COA5 c.-130G>C Benign ★★ same type
COA5 c.-69C>G Likely benign ★★ 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/coa5-p-pro9 (accessed [today's date]).

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