Is COL4A1 p.Pro890= (c.2670G>A) pathogenic?

COL4A1 p.Pro890= (c.2670G>A) is classified Likely benign in COL4A1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-01-21). Ultra-rare (popmax 0.0134%, eas); Associated with Inborn genetic diseases.

What condition is associated with COL4A1 p.Pro890= (c.2670G>A)?

COL4A1 p.Pro890= (c.2670G>A) is associated with Inborn genetic diseases (ClinVar).

How common is COL4A1 p.Pro890= (c.2670G>A) in the general population?

COL4A1 p.Pro890= (c.2670G>A) is ultra-rare (popmax 0.0134%, eas) (gnomAD).

COL4A1 p.Pro890=

c.2670G>A · rs769582266 · VCV2058771

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0134%, eas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -6.3	GERP -3.2
Overall
CADD	1.66	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0134% East Asian · 6/44,886 alleles

Filtering AF 0.00579% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00394%

Overall 0.00143% 23/1,613,992 alleles · ultra-rare exomes 17/1,461,872 · genomes 6/152,120 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0134%	7,481
South Asian	0.00329%	30,361
Remaining individualsnot grpmax-eligible	0.0016%	62,488
African / African-American	0.00134%	74,886
European (non-Finnish)	0.00102%	98,336

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: COL4A1
Protein: p.Pro890=
Coding: c.2670G>A
MANE Select: NM_001845
dbSNP: rs769582266
Type: single nucleotide variant
Location: chr13:110177888 (GRCh38)
Gene constraint: LOEUF 0.238 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 49.43 · 4 PDB
Residue 890: the 'triple-helical region' region; the 'disordered' region

Full COL4A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

COL4A1 p.Pro890Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
COL4A1 p.Gly1580Ser Pathogenic ★★ same condition
COL4A1 p.Gly755Arg Pathogenic ★★ same condition
COL4A1 p.Ala1628Thr Uncertain significance ★★ ⚠ same condition
COL4A1 p.Ala683Thr Uncertain significance ★★ ⚠ same condition
COL4A1 p.Ala806Val Uncertain significance ★★ ⚠ same condition
COL4A1 p.Arg1495His Uncertain significance ★★ ⚠ same condition
COL4A1 p.Arg1668Lys Uncertain significance ★★ ⚠ 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/col4a1-p-pro890 (accessed [today's date]).

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