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]

OMIM Research

OMIM ResearchGenerating clinical summary…

DNmechanismADLOEUF 1.031 OMIM phenotype

Clinical Summary— UBIAD1

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Population Constraint (gnomAD)

Low constraint (pLI 0.02) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

12 unique Pathogenic / Likely Pathogenic· 95 VUS of 139 total submissions

Explore recent and relevant literature in Research Assistant →

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

Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗

definitiveUBIAD1-related Schyder corneal dystrophyOTHERAD

This gene — mechanism propensity

0.7130th %ile

GOF

0.6346th %ile

LOF

0.2871th %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

139 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic9

Likely Pathogenic3

VUS95

Likely Benign5

Benign24

Conflicting2

Pathogenic

Likely Pathogenic

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	9	0	0	9
Likely Pathogenic	0	3	0	0	3
VUS	1	46	48	0	95
Likely Benign	0	2	1	2	5
Benign	0	2	16	6	24
Conflicting	—				2
Total	1	62	65	8	138

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

41 pathogenic / likely-pathogenic (of 60) ClinVar copy-number / structural variants overlap UBIAD1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →