Is COL4A3 p.Pro60fs (c.172_178dup) pathogenic?

COL4A3 p.Pro60fs (c.172178dup) is classified Pathogenic in COL4A3 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-03-21). Associated with Alport syndrome 3b, autosomal recessive.

What condition is associated with COL4A3 p.Pro60fs (c.172_178dup)?

COL4A3 p.Pro60fs (c.172_178dup) is associated with Alport syndrome 3b, autosomal recessive (ClinVar).

How is Alport syndrome inherited?

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

COL4A3 p.Pro60fs

c.172_178dup · VCV3391006

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

Alport syndrome 3b, autosomal recessive

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 3 of 52
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.7	GERP 1.8, phastCons 0.031

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

Variant & gene context

Gene: COL4A3
Protein: p.Pro60fs
Coding: c.172_178dup
MANE Select: NM_000091
Type: Duplication
Location: chr2:227240168 (GRCh38)
Gene constraint: LOEUF 0.709 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 48.64 · 2 PDB
Residue 60: the 'triple-helical region' region; the 'disordered' region

Full COL4A3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Alport syndrome 3b, autosomal recessive — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Alport syndrome (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked dominant
Onset: Adolescent, Adult, Childhood, Elderly

Similar variants

COL4A3 p.Gly1183dup Pathogenic/Likely pathogenic ★★ same condition
COL4A3 p.Gly807fs Pathogenic/Likely pathogenic ★★ same condition
COL4A3 p.Pro240fs Pathogenic/Likely pathogenic ★★ same condition
COL4A3 c.(3882+1_3883-1 Pathogenic ★ same condition
COL4A3 p.Asn1184fs Likely pathogenic ★ same condition
COL4A3 p.Gln1596fs Likely pathogenic ★ same condition
COL4A3 p.Gly1183fs Likely pathogenic ★ same condition
COL4A3 p.Gly913fs 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/col4a3-p-pro60fs (accessed [today's date]).

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