Is COL9A2 p.Pro123fs (c.368del) pathogenic?

COL9A2 p.Pro123fs (c.368del) is classified Pathogenic in COL9A2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-20). Absent from gnomAD.

How common is COL9A2 p.Pro123fs (c.368del) in the general population?

COL9A2 p.Pro123fs (c.368del) is absent from gnomAD (gnomAD).

COL9A2 p.Pro123fs

c.368del · rs2522557278 · VCV2023401

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 8 of 32
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -2	GERP -3.7

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: COL9A2
Protein: p.Pro123fs
Coding: c.368del
MANE Select: NM_001852
dbSNP: rs2522557278
Type: Deletion
Location: chr1:40312108 (GRCh38)
Gene constraint: LOEUF 0.817 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 54.99 · 4 PDB
Residue 123: the 'disordered' region; the 'triple-helical region 4 (col4)' region

Full COL9A2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

COL9A2 p.Pro123Ser Uncertain significance ★★ ⚠ same residue
COL9A2 p.Asn503fs Pathogenic/Likely pathogenic ★★ same type
COL9A2 p.Gly412fs Pathogenic ★★ same type
COL9A2 p.Gly415fs Pathogenic/Likely pathogenic ★★ same type
COL9A2 p.Leu537fs Pathogenic/Likely pathogenic ★★ same type
COL9A2 p.Lys243fs Pathogenic ★★ same type
COL9A2 c.1008+3_1008+6del Uncertain significance ★★ same type
COL9A2 c.1603+18del Benign/Likely 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/col9a2-p-pro123fs (accessed [today's date]).

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