Is COL4A3 p.Gly467Glu (c.1400G>A) pathogenic?

COL4A3 p.Gly467Glu (c.1400G>A) is classified Likely pathogenic in COL4A3 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-08). AlphaMissense: likely pathogenic (0.8201); Absent from gnomAD v4.1; Associated with autosomal dominant Alport syndrome.

What condition is associated with COL4A3 p.Gly467Glu (c.1400G>A)?

COL4A3 p.Gly467Glu (c.1400G>A) is associated with autosomal dominant Alport syndrome, Alport syndrome 3b, autosomal recessive, hematuria, benign familial, 2 (ClinVar).

How common is COL4A3 p.Gly467Glu (c.1400G>A) in the general population?

COL4A3 p.Gly467Glu (c.1400G>A) is absent from gnomAD v4.1 (gnomAD).

How is Alport syndrome inherited?

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

What do computational predictors say about COL4A3 p.Gly467Glu (c.1400G>A)?

AlphaMissense predicts likely pathogenic (score 0.8201) — an in-silico prediction, not a clinical call.

COL4A3 p.Gly467Glu

c.1400G>A · VCV3586021

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8201 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

autosomal dominant Alport syndrome

Computational evidence

Protein change
AlphaMissense	0.8201	likely pathogenic ✓ concordant with ClinVar · top 7% in COL4A3
REVEL	0.947	strongly pathogenic-leaning
SaProt	LLR -14.32	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.6, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 58 kb · p 2.1e-11 · regional, not allelic
Overall
CADD	25.3	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: COL4A3
Protein: p.Gly467Glu
Coding: c.1400G>A
MANE Select: NM_000091
Type: single nucleotide variant
Location: chr2:227266501 (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 467: the 'triple-helical region' region; the 'disordered' region

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

Disease context

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

Also linked: Alport syndrome 3b, autosomal recessive hematuria, benign familial, 2

For Alport syndrome (Orphanet):

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

Similar variants

COL4A3 p.Gly467= Likely benign ★ same residue
COL4A3 c.1114+1G>A Likely pathogenic ★★ same condition
COL4A3 c.1114+2T>C Pathogenic/Likely pathogenic ★★ same condition
COL4A3 c.1408+1G>C Pathogenic/Likely pathogenic ★★ same condition
COL4A3 c.2656+1G>T Pathogenic/Likely pathogenic ★★ same condition
COL4A3 c.2746+1G>T Pathogenic ★★ same condition
COL4A3 c.2747-1G>C Likely pathogenic ★★ same condition
COL4A3 c.279+1G>A 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-gly467glu (accessed [today's date]).

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