UBIAD1

Chr 1AD

UbiA prenyltransferase domain containing 1

Also known as: SCCD, TERE1

NCBI Gene: 29914 ENSG00000120942 UniProt: Q9Y5Z9 OMIM: 611632

This gene encodes a protein thought to be involved in cholesterol and phospholipid metabolism. Mutations in this gene are associated with Schnyder crystalline corneal dystrophy. [provided by RefSeq, Oct 2008]

GeneReviews OMIM Research

GeneReviews OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Corneal dystrophy, Schnyder typeMIM #121800

Clinical highlights

Gene–disease validity

Not independently assessedOMIM lists Corneal dystrophy, Schnyder type; no ClinGen or GenCC tier

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.03

LOEUF

Mechanism· predicted

📖

GeneReview available — UBIAD1

Authoritative clinical overview · Recommended first read

Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.03LOEUF

pLI 0.020

Z-score 1.53

OE 0.45 (0.22–1.03)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

1.12Z-score

OE missense 0.76 (0.67–0.88)

137 obs / 179.1 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.45 (0.22–1.03)

0≤0.351.4

Missense OE?0.76 (0.67–0.88)

0≤0.61.4

Synonymous OE?1.26

0≤1.21.6

LoF obs/exp: 4 / 8.9Missense obs/exp: 137 / 179.1Syn Z: -1.89

Background carrier burden — how many people carry a rare variant somewhere in UBIAD1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 270

360 rare PASS variants

Rare truncating (LoF)

1 in 4,600

51 rare PASS variants

Rare synonymous (reference)

1 in 180

218 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for UBIAD1. 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 360	1 in 7,400
South Asian	~43k	1 in 170	1 in 1,100
Remaining (unassigned)	~30k	1 in 210	≈ 1 in 6,100
European (Finnish)	~27k	1 in 330	≈ 1 in 27,000
Admixed American	~22k	1 in 240	≈ 1 in 22,000
African / African American	~21k	1 in 160	≈ 1 in 4,900
East Asian	~20k	1 in 370	1 in 850
Ashkenazi Jewish	~13k	1 in 460	none seen
Middle Eastern	~2,884	1 in 260	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 2 coding exons well covered in gnomAD exomes and genomes.? see exons ↓