Is COL6A2 p.Arg862= (c.2584C>A) pathogenic?

COL6A2 p.Arg862= (c.2584C>A) is classified Likely benign in COL6A2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-31). Absent from gnomAD v4.1; Associated with Bethlem myopathy 1A.

What condition is associated with COL6A2 p.Arg862= (c.2584C>A)?

COL6A2 p.Arg862= (c.2584C>A) is associated with Bethlem myopathy 1A (ClinVar).

How common is COL6A2 p.Arg862= (c.2584C>A) in the general population?

COL6A2 p.Arg862= (c.2584C>A) is absent from gnomAD v4.1 (gnomAD).

How is Bethlem muscular dystrophy inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

COL6A2 p.Arg862=

c.2584C>A · rs777822883 · VCV1941975

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 1,602,920)

Conditions

Bethlem myopathy 1A

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 0.38	GERP 0.3, phastCons 0.98
Overall
CADD	1.293	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,602,920). 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: COL6A2
Protein: p.Arg862=
Coding: c.2584C>A
MANE Select: NM_001849
dbSNP: rs777822883
Type: single nucleotide variant
Location: chr21:46132076 (GRCh38)
Gene constraint: LOEUF 0.895 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 69.58 · 1 PDB
Residue 862: the vwfa 3 domain; an α-helix; the 'nonhelical region' region

Full COL6A2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Bethlem myopathy 1A — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Bethlem muscular dystrophy (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive
Onset: Childhood, Infancy
Prevalence: 1-9 / 1 000 000 (United Kingdom)

Similar variants

COL6A2 p.Arg862Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
COL6A2 p.Arg862Trp Conflicting classifications of pathogenicity ★ ⚠ same residue
COL6A2 c.1000-1G>T Pathogenic ★★ same condition
COL6A2 c.1000-2A>C Pathogenic ★★ same condition
COL6A2 c.1053+1G>A Pathogenic ★★ same condition
COL6A2 c.1053+1G>C Pathogenic/Likely pathogenic ★★ same condition
COL6A2 c.1053+2T>C Pathogenic/Likely pathogenic ★★ same condition
COL6A2 c.1054-2A>G 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/col6a2-p-arg862 (accessed [today's date]).

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