Is COL4A5 p.Lys155= (c.465G>A) pathogenic?

COL4A5 p.Lys155= (c.465G>A) is classified Uncertain significance in COL4A5 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2023-03-09). Absent from gnomAD v4.1; Associated with kidney disorder.

What condition is associated with COL4A5 p.Lys155= (c.465G>A)?

COL4A5 p.Lys155= (c.465G>A) is associated with kidney disorder (ClinVar).

How common is COL4A5 p.Lys155= (c.465G>A) in the general population?

COL4A5 p.Lys155= (c.465G>A) is absent from gnomAD v4.1 (gnomAD).

COL4A5 p.Lys155=

c.465G>A · rs2524210043 · VCV1712420

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,183,080)

Conditions

kidney disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.72	acceptor loss · deltas
Pangolin	Δ0.62	loss · gain 0.12 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 12	GERP 1.7, phastCons 1
Overall
CADD	23.4	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,183,080). 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.Lys155=
Coding: c.465G>A
MANE Select: NM_033380
dbSNP: rs2524210043
Type: single nucleotide variant
Location: chrX:108571837 (GRCh38)
Structure: AlphaFold pLDDT 49.04 · 2 PDB
Residue 155: the 'triple-helical region' region; the 'disordered' region

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

Disease context

kidney disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

COL4A5 p.Arg1569Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
COL4A5 p.Asn1010Ser Benign/Likely benign ★★ same condition
COL4A5 p.Gly1173= Benign ★★ same condition
COL4A5 p.Gly1500= Benign/Likely benign ★★ same condition
COL4A5 p.Gln22= Conflicting classifications of pathogenicity ★ same condition
COL4A5 p.Gly953Val Conflicting classifications of pathogenicity ★ ⚠ same condition
COL4A5 p.Met1553Ile Conflicting classifications of pathogenicity ★ ⚠ same condition
COL4A5 p.Pro1396fs 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-lys155 (accessed [today's date]).

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