Is COL6A2 p.Ala698Val (c.2093_2094delinsTA) pathogenic?

COL6A2 p.Ala698Val (c.20932094delinsTA) is classified Uncertain significance in COL6A2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-07). Absent from gnomAD; Associated with Bethlem myopathy 1A.

What condition is associated with COL6A2 p.Ala698Val (c.2093_2094delinsTA)?

COL6A2 p.Ala698Val (c.2093_2094delinsTA) is associated with Bethlem myopathy 1A (ClinVar).

How common is COL6A2 p.Ala698Val (c.2093_2094delinsTA) in the general population?

COL6A2 p.Ala698Val (c.2093_2094delinsTA) is absent from gnomAD (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.Ala698Val

c.2093_2094delinsTA · rs2517017708 · VCV1991990

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 · substitutions only
Constraint at this position
Conservation	phyloP 7.5	GERP 1.3, phastCons 1
Regional constraint	o/e 1.16	unconstrained · MANE · 16 kb · p 1.4e-07 · regional, not allelic

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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.Ala698Val
Coding: c.2093_2094delinsTA
MANE Select: NM_001849
dbSNP: rs2517017708
Type: Indel
Location: chr21:46125908 (GRCh38)
Gene constraint: LOEUF 0.895 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 69.58 · 1 PDB
Residue 698: the vwfa 2 domain; 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.Ala698= Benign ★★ same residue
COL6A2 c.955-3_955-1delinsAA Likely pathogenic ★ same condition
COL6A2 c.999+9_1053+32delinsGCTGAAGGAGGGGTGCAAACGGCCCTTACCCGGTTTCCAGGGTCTCCCTTGCAGCCTTCA Pathogenic ★ same condition
COL6A2 p.Gly700Ser Pathogenic ★ same condition
COL6A2 c.1671+10_1671+11delinsGA Uncertain significance ★ same condition
COL6A2 p.Arg993His Uncertain significance ★ same condition
COL6A2 p.Glu565Arg Uncertain significance ★ same condition
COL6A2 p.Gly346Val Conflicting classifications of pathogenicity ★ 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-ala698val (accessed [today's date]).

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