COL4A1

Chr 13AD

collagen type IV alpha 1 chain

Also known as: BSVD, BSVD1, COL4A1s, PADMAL, RATOR

The encoded type IV collagen alpha protein functions as part of a heterotrimer that forms integral components of basement membranes and interacts with other extracellular matrix components including perlecans, proteoglycans, and laminins. Mutations cause autosomal dominant conditions including hereditary angiopathy with nephropathy, aneurysms and muscle cramps, brain small vessel disease with or without ocular anomalies, and pontine microangiopathy with leukoencephalopathy. The pathogenic mechanism involves loss of function, leading to compromised basement membrane integrity in cerebrovascular and other tissues.

OMIMResearchSummary from RefSeq, OMIM, UniProt, Mechanism
DNmechanismADLOEUF 0.135 OMIM phenotypes
Clinical SummaryCOL4A1
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Gene-Disease Validity (ClinGen)
COL4A1-related disorder · ADDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
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Clinical Trials
2 active or recruiting trials — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

LoF intolerant — likely haploinsufficient
LoF Constraint
0.13LOEUF
pLI 1.000
Z-score 8.32
OE 0.07 (0.040.13)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint
3.02Z-score
OE missense 0.73 (0.680.77)
701 obs / 964.9 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios
LoF OE0.07 (0.040.13)
00.351.4
Missense OE0.73 (0.680.77)
00.61.4
Synonymous OE1.20
01.21.6
LoF obs/exp: 6 / 92.3Missense obs/exp: 701 / 964.9Syn Z: -2.97
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveCOL4A1-related porencephaly and brain small vessel disease with or without ocular anomaliesDNAD
DN
0.5477th %ile
GOF
0.3788th %ile
LOF
0.70top 10%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · 1 literature citation · LOEUF 0.13

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Literature Evidence

LOFNovel COL4A1 mutations cause cerebral small vessel disease by haploinsufficiency.PMID:23065703

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

COL4A1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold
Clinical Literature
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Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗