Is COL4A5 p.Arg1472Pro (c.4415_4416delinsCT) pathogenic?

COL4A5 p.Arg1472Pro (c.44154416delinsCT) is classified Conflicting classifications of pathogenicity in COL4A5 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2026-01-08). Absent from gnomAD; Associated with X-linked Alport syndrome.

What condition is associated with COL4A5 p.Arg1472Pro (c.4415_4416delinsCT)?

COL4A5 p.Arg1472Pro (c.4415_4416delinsCT) is associated with X-linked Alport syndrome (ClinVar).

How common is COL4A5 p.Arg1472Pro (c.4415_4416delinsCT) in the general population?

COL4A5 p.Arg1472Pro (c.4415_4416delinsCT) is absent from gnomAD (gnomAD).

How is Alport syndrome inherited?

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

COL4A5 p.Arg1472Pro

c.4415_4416delinsCT · rs2147991408 · VCV1482498

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

X-linked Alport syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 2.9, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 256 kb · p 6e-09 · regional, not allelic

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: COL4A5
Protein: p.Arg1472Pro
Coding: c.4415_4416delinsCT
MANE Select: NM_033380
dbSNP: rs2147991408
Type: Indel
Location: chrX:108687581 (GRCh38)
Structure: AlphaFold pLDDT 49.04 · 2 PDB
Residue 1472: the collagen iv nc1 domain; a β-strand

Full COL4A5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

X-linked Alport syndrome — 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

COL4A5 p.Arg1472Cys Uncertain significance ★★ ⚠ same residue
COL4A5 p.Arg1472Leu Uncertain significance ⚠ same residue
COL4A5 c.1949-3_1949delinsAGGATCCCCTGGA Likely pathogenic ★ same condition
COL4A5 c.2509_2509+1delinsTT Likely pathogenic ★ same condition
COL4A5 c.646-4_646-2delinsTCT Likely pathogenic ★ same condition
COL4A5 p.Gly1345Val Likely pathogenic ★ same condition
COL4A5 p.Gly1354Asp Likely pathogenic ★ same condition
COL4A5 p.Gly150Asp 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/col4a5-p-arg1472pro (accessed [today's date]).

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