Is COL4A4 p.Ser32fs (c.93_94del) pathogenic?

COL4A4 p.Ser32fs (c.9394del) is classified Pathogenic in COL4A4 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-11-12). Very rare (popmax 8.5e-05%, nfe); Associated with hematuria, benign familial, 1.

What condition is associated with COL4A4 p.Ser32fs (c.93_94del)?

COL4A4 p.Ser32fs (c.93_94del) is associated with hematuria, benign familial, 1 (ClinVar).

How common is COL4A4 p.Ser32fs (c.93_94del) in the general population?

COL4A4 p.Ser32fs (c.93_94del) is very rare (popmax 8.5e-05%, nfe) (gnomAD).

COL4A4 p.Ser32fs

c.93_94del · rs1360606073 · VCV2008694

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 8.5e-05%, nfe)

Conditions

hematuria, benign familial, 1

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 48
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.4	GERP 2.5, phastCons 1

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.5e-05% European (non-Finnish) · 1/1,176,778 alleles

Overall 6.86e-05% 1/1,458,106 alleles · very rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: COL4A4
Protein: p.Ser32fs
Coding: c.93_94del
MANE Select: NM_000092
dbSNP: rs1360606073
Type: Deletion
Location: chr2:227144536 (GRCh38)
Gene constraint: LOEUF 0.607 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 49.03 · 2 PDB

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

Disease context

hematuria, benign familial, 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

COL4A4 c.1321_1369+3del Pathogenic/Likely pathogenic ★★ same condition
COL4A4 c.2385del Pathogenic/Likely pathogenic ★★ same condition
COL4A4 c.327+1_327+5del Likely pathogenic ★★ same condition
COL4A4 c.4091-8_4092del Likely pathogenic ★★ same condition
COL4A4 p.Arg877_Gly888del Likely pathogenic ★★ same condition
COL4A4 p.Asn464fs Pathogenic/Likely pathogenic ★★ same condition
COL4A4 p.Glu1104fs Pathogenic/Likely pathogenic ★★ same condition
COL4A4 p.Gly1060fs 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/col4a4-p-ser32fs (accessed [today's date]).

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