COL15A1

Chr 9

collagen type XV alpha 1 chain

The protein forms type XV collagen, which stabilizes microvessels and muscle cells in both cardiac and skeletal muscle by adhering basement membranes to underlying connective tissue. Mutations cause autosomal recessive muscle-eye-brain disease with multicentric core disease, characterized by congenital muscular dystrophy, structural eye abnormalities, and intellectual disability. The gene is highly constrained against loss-of-function variants, indicating that complete loss of protein function is likely pathogenic.

OMIMResearchSummary from RefSeq, UniProt
DNmechanismLOEUF 0.50
Clinical SummaryCOL15A1
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Moderate LoF intolerance
LoF Constraint
0.50LOEUF
pLI 0.000
Z-score 5.05
OE 0.37 (0.270.50)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
0.12Z-score
OE missense 0.99 (0.931.05)
798 obs / 807.6 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.37 (0.270.50)
00.351.4
Missense OE0.99 (0.931.05)
00.61.4
Synonymous OE1.06
01.21.6
LoF obs/exp: 27 / 73.8Missense obs/exp: 798 / 807.6Syn Z: -0.90
DN
0.6648th %ile
GOF
0.4874th %ile
LOF
0.3356th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

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.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

COL15A1 · 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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