GeneBe

UBIAD1

protein-coding

UbiA prenyltransferase domain containing 1

Gene summary

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]

Previous symbols:
  • SCCD

MANE transcript

NM_013319.3

Inheritance

AD

ClinVar variants

P:12U:51B:14

Top phenotype

Schnyder corneal dystrophy

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr1:11,273,198-11,296,049

External References & Databases

Ensembl (ENSG00000120942)NCBI Gene (29914)OMIM (611632)HGNC:30791GenCCUniProt (Q9Y5Z9)AlphaFoldClinVar (UBIAD1)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~22.9 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Schnyder corneal dystrophySTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007374

Submitter: Ambry Genetics

Schnyder corneal dystrophySTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007374

Submitter: PanelApp Australia

Schnyder corneal dystrophySUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007374

Submitter: Orphanet

Schnyder corneal dystrophySTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007374

Submitter: Labcorp Genetics (formerly Invitae)

Schnyder corneal dystrophyDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007374

Submitter: G2P

Clinical Genomic Database (CGD)

Schnyder corneal dystrophyAD

Manifestation: Ophthalmologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Comments: Phototherapeutic keratectomy has been described as beneficial in this type of corneal dystrophy, though the advantage of early (genetic) diagnosis is unclear

Refs: 3486394; 8190477; 9450854; 10442892; 15034782; 17668063; 17962451; 18176953; 19429578; 19649163; 20489584; 20505825; 22065921Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to UBIAD1 variants in ClinVar

5 Conditions Cataloged
not specifiedTotal: 39
Schnyder crystalline corneal dystrophyTotal: 32
not providedTotal: 17
UBIAD1-related disorderTotal: 2
Corneal dystrophyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_013319.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
6
clinvar
 8
missense
9
clinvar
3
clinvar
50
clinvar
4
clinvar
2
clinvar
 68
nonsense
1
clinvar
 1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total93516877

Highest pathogenic variant AF is 0.0000065715976

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_013319.3RefSeqNP_037451.12MANE Select
ENST00000376810.6EnsemblENSP00000366006.52MANE Select
NM_001330349.2RefSeqNP_001317278.13Standard
NM_001330350.2RefSeqNP_001317279.12Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
ubiad1Danio rerio

Structure: blood vessel endothelial cell

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Metabolism of fat-soluble vitamins
  • Metabolism
  • Metabolism of vitamins and cofactors
  • Metabolism of vitamin K

Biological Process

  • ubiquinone biosynthetic process
  • menaquinone biosynthetic process
  • ubiquinone biosynthetic process via 3,4-dihydroxy-5-polyprenylbenzoate
  • vitamin K biosynthetic process
  • vitamin K metabolic process

Molecular Function

  • prenyltransferase activity
  • protein binding
  • antioxidant activity

Cellular Component

  • nucleus
  • cytoplasm
  • endoplasmic reticulum
  • endoplasmic reticulum membrane
  • membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000376810
Coding exons
2
Length
22844
Individuals with no LoFs
125726
Homozygous LoFs
0
Heterozygous LoFs
22
Defined
125748
p
0.0000875
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.121371790.7650.000009502165
Missense (PolyPhen)2347.5980.48321600
Synonymous-1.8910684.01.260.00000494765
Loss of Function1.5348.920.4484.61e-7102

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian0.000270.00027rare
Finnish00.0absent
European (Non-Finnish)0.0000970.000097rare
South Asian0.000200.00020rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Prenyltransferase that mediates the formation of menaquinone-4 (MK-4) and coenzyme Q10. MK-4 is a vitamin K2 isoform present at high concentrations in the brain, kidney and pancreas, and is required for endothelial cell development. Mediates the conversion of phylloquinone (PK) into MK-4, probably by cleaving the side chain of phylloquinone (PK) to release 2- methyl-1,4-naphthoquinone (menadione; K3) and then prenylating it with geranylgeranyl pyrophosphate (GGPP) to form MK-4. Also plays a role in cardiovascular development independently of MK-4 biosynthesis, by acting as a coenzyme Q10 biosynthetic enzyme: coenzyme Q10, also named ubiquinone, plays a important antioxidant role in the cardiovascular system. Mediates biosynthesis of coenzyme Q10 in the Golgi membrane, leading to protect cardiovascular tissues from NOS3/eNOS-dependent oxidative stress. {ECO:0000269|PubMed:20953171, ECO:0000269|PubMed:23374346}.;

Recessive Scores

pRec
0.189

Intolerance Scores

LoFtool
0.182
RVIS EVS
-0.12
RVIS percentile EVS
45.13

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
S
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.231

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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