Is COL1A2 p.Pro134fs (c.401del) pathogenic?

COL1A2 p.Pro134fs (c.401del) is classified Likely pathogenic in COL1A2 (ClinVar, Single submitter, 1 submitter; last evaluated 2016-08-30). Absent from gnomAD.

How common is COL1A2 p.Pro134fs (c.401del) in the general population?

COL1A2 p.Pro134fs (c.401del) is absent from gnomAD (gnomAD).

COL1A2 p.Pro134fs

c.401del · rs1057518136 · VCV373007

Likely pathogenic Single submitter

Classification

Likely 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 in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 9 of 52
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.34	GERP 1, 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: COL1A2
Protein: p.Pro134fs
Coding: c.401del
MANE Select: NM_000089
dbSNP: rs1057518136
Type: Deletion
Location: chr7:94404860 (GRCh38)
Gene constraint: LOEUF 0.339 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 55.02 · 5 PDB
Residue 134: the 'disordered' region

Full COL1A2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

COL1A2 p.Pro134= Likely benign ★★ same residue
COL1A2 c.2943+1_2943+2del Pathogenic ★★ same type
COL1A2 c.432+4_432+7del Pathogenic/Likely pathogenic ★★ same type
COL1A2 c.487-4_501del Pathogenic ★★ same type
COL1A2 p.Gly286fs Pathogenic ★★ same type
COL1A2 p.Pro1092fs Pathogenic ★★ same type
COL1A2 p.Tyr1178_Asp1181del Uncertain significance ★★ same type
COL1A2 c.1252-7del 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/col1a2-p-pro134fs (accessed [today's date]).

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