Is COL6A3 p.Arg3043= (c.9129C>T) pathogenic?

COL6A3 p.Arg3043= (c.9129C>T) is classified Benign in COL6A3 (ClinVar, Multiple submitters, 12 submitters; last evaluated 2026-02-03). Common (popmax 18.1%, afr) — too common for a highly-penetrant pathogenic allele; Associated with collagen 6-related myopathy.

What condition is associated with COL6A3 p.Arg3043= (c.9129C>T)?

COL6A3 p.Arg3043= (c.9129C>T) is associated with collagen 6-related myopathy, Bethlem myopathy 1A (ClinVar).

COL6A3 p.Arg3043=

Q: How common is COL6A3 p.Arg3043= (c.9129C>T) in the general population?

COL6A3 p.Arg3043= (c.9129C>T) is common (popmax 18.1%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.9129C>T · rs10201909 · VCV95017

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 12 submitters

gnomAD v4.1

Common

common (popmax 18.1%, afr) — too common for a highly-penetrant pathogenic allele

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 -9.6	GERP -3.2
Overall
CADD	0.062	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 18.1% African / African-American · 13,587/74,942 alleles

Filtering AF 17.9% ClinGen BA1/BS1 input FAF95, joint · FAF99 17.8%

Overall 2.61% 42,177/1,613,994 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	18.1%	6
Middle Eastern	6.29%	16
Remaining individualsnot grpmax-eligible	3.25%	31
Ashkenazi Jewishnot grpmax-eligible	3.25%	31
Admixed American	2.85%	35
South Asian	2.5%	40
European (non-Finnish)	1.74%	57
Finnishnot grpmax-eligible	0.862%	116
East Asian	0.214%	467

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.Arg3043=
Coding: c.9129C>T
MANE Select: NM_004369
dbSNP: rs10201909
Type: single nucleotide variant
Location: chr2:237334726 (GRCh38)
Gene constraint: LOEUF 0.564 · pLI <0.01 (gnomAD)
Residue 3043: a UniProt-annotated variant site (in dyt27); the fibronectin type-iii domain; 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.Arg3043His Benign/Likely benign ★★ same residue
COL6A3 p.Arg3043Cys Conflicting classifications of pathogenicity ★ ⚠ 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

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-arg3043 (accessed [today's date]).

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