Is COL11A2 p.Cys7fs (c.20_21del) pathogenic?

COL11A2 p.Cys7fs (c.2021del) is classified Pathogenic in COL11A2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-02). Absent from gnomAD.

How common is COL11A2 p.Cys7fs (c.20_21del) in the general population?

COL11A2 p.Cys7fs (c.20_21del) is absent from gnomAD (gnomAD).

COL11A2 p.Cys7fs

c.20_21del · rs2535614756 · VCV2763938

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 1 of 66
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.8	GERP 1.3, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

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: COL11A2
Protein: p.Cys7fs
Coding: c.20_21del
MANE Select: NM_080680
dbSNP: rs2535614756
Type: Deletion
Location: chr6:33192220 (GRCh38)
Gene constraint: LOEUF 0.503 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 50.18

Full COL11A2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

COL11A2 p.Gly922fs Pathogenic ★★ same type
COL11A2 p.Ile1223fs Pathogenic/Likely pathogenic ★★ same type
COL11A2 p.Pro897fs Pathogenic/Likely pathogenic ★★ same type
COL11A2 p.Glu301del Uncertain significance ★★ same type
COL11A2 c.1359+17del Likely benign ★★ same type
COL11A2 c.1819-18_1819-9del Likely benign ★★ same type
COL11A2 c.2116-14_2116-10del Likely benign ★★ same type
COL11A2 c.2431-18del 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/col11a2-p-cys7fs (accessed [today's date]).

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