COL20A1

Chr 20

collagen type XX alpha 1 chain

NCBI Gene: 57642 ENSG00000101203 UniProt: Q9P218 OMIM: 619390

Collagen XX alpha 1 chain forms collagen trimers in the extracellular matrix and is found in the endoplasmic reticulum and extracellular regions. Mutations cause corneal intraepithelial dyskeratosis with an autosomal dominant inheritance pattern. The gene shows low constraint against loss-of-function variants.

OMIM ResearchSummary from RefSeq, UniProt

Predicted to be located in endoplasmic reticulum lumen and extracellular matrix. Predicted to be part of collagen type XX trimer. [provided by Alliance of Genome Resources, Jun 2026]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.20

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.20LOEUF

pLI 0.000

Z-score 0.19

OE 0.97 (0.79–1.20)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.45Z-score

OE missense 1.05 (0.99–1.11)

778 obs / 743.1 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.97 (0.79–1.20)

0≤0.351.4

Missense OE?1.05 (0.99–1.11)

0≤0.61.4

Synonymous OE?1.17

0≤1.21.6

LoF obs/exp: 62 / 63.6Missense obs/exp: 778 / 743.1Syn Z: -2.49

Background carrier burden — how many people carry a rare variant somewhere in COL20A1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 20

2,059 rare PASS variants

Rare truncating (LoF)

1 in 220

409 rare PASS variants

Rare synonymous (reference)

1 in 35

937 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for COL20A1. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 29	1 in 270
South Asian	~43k	1 in 18	1 in 220
Remaining (unassigned)	~30k	1 in 16	1 in 170
European (Finnish)	~27k	1 in 89	1 in 300
Admixed American	~22k	1 in 20	1 in 190
African / African American	~21k	1 in 20	1 in 150
East Asian	~20k	1 in 23	1 in 280
Ashkenazi Jewish	~13k	1 in 140	1 in 1,000
Middle Eastern	~2,884	1 in 18	1 in 160

Each group is summed over the variants that are rare in that group. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 30 of 34 coding exons well covered in gnomAD exomes; exons 9, 26, 27, 31 marginal. Genomes: all 34.? see exons ↓