Is COL4A2 p.Pro1643= (c.4929G>A) pathogenic?

COL4A2 p.Pro1643= (c.4929G>A) is classified Benign/Likely benign in COL4A2 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-22). Rare (popmax 0.481%, afr); Associated with brain small vessel disease 2A, autosomal dominant.

What condition is associated with COL4A2 p.Pro1643= (c.4929G>A)?

COL4A2 p.Pro1643= (c.4929G>A) is associated with brain small vessel disease 2A, autosomal dominant (ClinVar).

How common is COL4A2 p.Pro1643= (c.4929G>A) in the general population?

COL4A2 p.Pro1643= (c.4929G>A) is rare (popmax 0.481%, afr) (gnomAD).

COL4A2 p.Pro1643=

c.4929G>A · rs7320105 · VCV311192

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

rare (popmax 0.481%, afr)

Conditions

brain small vessel disease 2A, autosomal dominant

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 -9.3	GERP -3.8
Overall
CADD	1.01	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.481% African / African-American · 361/75,054 alleles

Filtering AF 0.44% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.424%

Overall 0.187% 3,013/1,613,530 alleles · rare exomes 2,583/1,461,180 · genomes 430/152,350 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.481%	208
Ashkenazi Jewishnot grpmax-eligible	0.48%	208
European (non-Finnish)	0.19%	525
Remaining individualsnot grpmax-eligible	0.182%	548
Finnishnot grpmax-eligible	0.163%	615
Admixed American	0.07%	1,429
Middle Eastern	0.0165%	6,060
East Asian	0.00446%	22,444
South Asian	0.0011%	91,078

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: COL4A2
Protein: p.Pro1643=
Coding: c.4929G>A
MANE Select: NM_001846
dbSNP: rs7320105
Type: single nucleotide variant
Location: chr13:110511981 (GRCh38)
Gene constraint: LOEUF 0.618 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 47.97 · 4 PDB
Residue 1643: the collagen iv nc1 domain; an α-helix

Full COL4A2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

brain small vessel disease 2A, autosomal dominant — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

COL4A2 p.Pro1643Leu Uncertain significance ★★ ⚠ same residue
COL4A2 c.361-1G>A Pathogenic/Likely pathogenic ★★ same condition
COL4A2 p.Gly619Asp Likely pathogenic ★★ same condition
COL4A2 c.2425+3G>A Uncertain significance ★★ same condition
COL4A2 p.Ala370Pro Uncertain significance ★★ ⚠ same condition
COL4A2 p.Ala95Asp Uncertain significance ★★ ⚠ same condition
COL4A2 p.Arg1069Gln Uncertain significance ★★ ⚠ same condition
COL4A2 p.Arg1069Trp 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/col4a2-p-pro1643 (accessed [today's date]).

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