Is COL4A4 p.Ala401fs (c.1200dup) pathogenic?

COL4A4 p.Ala401fs (c.1200dup) is classified Pathogenic in COL4A4 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-04-21). Absent from gnomAD.

How common is COL4A4 p.Ala401fs (c.1200dup) in the general population?

COL4A4 p.Ala401fs (c.1200dup) is absent from gnomAD (gnomAD).

COL4A4 p.Ala401fs

c.1200dup · rs2150739132 · VCV1404025

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 19 of 48
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.1	GERP -2.2, phastCons 0.061

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: COL4A4
Protein: p.Ala401fs
Coding: c.1200dup
MANE Select: NM_000092
dbSNP: rs2150739132
Type: Duplication
Location: chr2:227098697 (GRCh38)
Gene constraint: LOEUF 0.607 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 49.03 · 2 PDB
Residue 401: the 'triple-helical region' region

Full COL4A4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

COL4A4 p.Ala401Val Benign/Likely benign ★★ same residue
COL4A4 p.Ala401= Conflicting classifications of pathogenicity ★ same residue
COL4A4 p.Ala401Pro Uncertain significance ★ ⚠ same residue
COL4A4 p.Ala1546fs Pathogenic/Likely pathogenic ★★ same type
COL4A4 p.Arg1114fs Pathogenic/Likely pathogenic ★★ same type
COL4A4 p.Cys1588fs Pathogenic/Likely pathogenic ★★ same type
COL4A4 p.Gln1105fs Pathogenic/Likely pathogenic ★★ same type
COL4A4 p.Gly226fs Pathogenic/Likely pathogenic ★★ 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/col4a4-p-ala401fs (accessed [today's date]).

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