Is COL6A3 p.Phe2795= (c.8385C>T) pathogenic?

COL6A3 p.Phe2795= (c.8385C>T) is classified Benign/Likely benign in COL6A3 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-05-18). Rare (popmax 0.379%, eas); Associated with collagen 6-related myopathy.

What condition is associated with COL6A3 p.Phe2795= (c.8385C>T)?

COL6A3 p.Phe2795= (c.8385C>T) is associated with collagen 6-related myopathy, Bethlem myopathy 1A (ClinVar).

How common is COL6A3 p.Phe2795= (c.8385C>T) in the general population?

COL6A3 p.Phe2795= (c.8385C>T) is rare (popmax 0.379%, eas) (gnomAD).

COL6A3 p.Phe2795=

c.8385C>T · rs201460305 · VCV335099

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.379%, eas)

Conditions

collagen 6-related myopathy

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 9.8	GERP 1.7, phastCons 1
Overall
CADD	9.633	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.379% East Asian · 170/44,878 alleles

Filtering AF 0.332% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.314%

Overall 0.0107% 172/1,614,200 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.379%	264
Remaining individualsnot grpmax-eligible	0.0016%	62,510
European (non-Finnish)	8.47e-05%	1,180,043

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: COL6A3
Protein: p.Phe2795=
Coding: c.8385C>T
MANE Select: NM_004369
dbSNP: rs201460305
Type: single nucleotide variant
Location: chr2:237340531 (GRCh38)
Gene constraint: LOEUF 0.564 · pLI <0.01 (gnomAD)
Residue 2795: the vwfa 12 domain; a β-strand; the 'nonhelical region' region

Full COL6A3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Also linked: Bethlem myopathy 1A

Similar variants

COL6A3 p.Phe2795Ser Uncertain significance ★★ ⚠ same residue
COL6A3 c.5838+1G>T Pathogenic/Likely pathogenic ★★ same condition
COL6A3 c.6156+1G>A Pathogenic ★★ same condition
COL6A3 c.6157-2A>C Pathogenic ★★ same condition
COL6A3 c.6210+1G>A Pathogenic ★★ same condition
COL6A3 c.6282+1G>A Pathogenic ★★ same condition
COL6A3 c.6282+1G>C Pathogenic/Likely pathogenic ★★ same condition
COL6A3 c.6309+1G>A 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/col6a3-p-phe2795 (accessed [today's date]).

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