UBIAD1

UbiA prenyltransferase domain containing 1

Basic information

Region (hg38): 1:11273197-11296049

Previous symbols: [ "SCCD" ]

Links

ENSG00000120942 ∙ NCBI:29914 ∙ OMIM:611632 ∙ HGNC:30791 ∙ Uniprot:Q9Y5Z9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Schnyder corneal dystrophy (Strong), mode of inheritance: AD
• Schnyder corneal dystrophy (Supportive), mode of inheritance: AD
• Schnyder corneal dystrophy (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Schnyder corneal dystrophy	AD	General	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	Ophthalmologic	3486394; 8190477; 9450854; 10442892; 15034782; 17668063; 17962451; 18176953; 19429578; 19649163; 20489584; 20505825; 22065921
Phototherapeutic keratectomy has been described as beneficial in this type of corneal dystrophy, though the advantage of early (genetic) diagnosis is unclear

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the UBIAD1 gene.

• Schnyder crystalline corneal dystrophy (85 variants)
• Inborn genetic diseases (7 variants)
• not provided (6 variants)
• UBIAD1-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBIAD1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	6	7
missense		1	14	3	2	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			49		18	67
Total	0	1	63	4	26

Highest pathogenic variant AF is 0.00000657

Variants in UBIAD1

This is a list of pathogenic ClinVar variants found in the UBIAD1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-11273221-C-T		Schnyder crystalline corneal dystrophy	Uncertain significance (Jan 13, 2018)
1-11273222-C-T		Schnyder crystalline corneal dystrophy	Uncertain significance (Apr 27, 2017)
1-11273337-G-A		Schnyder crystalline corneal dystrophy	Benign (Jan 13, 2018)
1-11273428-G-A		Schnyder crystalline corneal dystrophy	Uncertain significance (Jan 13, 2018)
1-11273446-G-C		Schnyder crystalline corneal dystrophy	Uncertain significance (Mar 30, 2018)
1-11273454-G-C		Schnyder crystalline corneal dystrophy	Uncertain significance (Mar 23, 2018)
1-11273485-T-G		Schnyder crystalline corneal dystrophy	Benign (Jan 12, 2018)
1-11273528-T-C		Schnyder crystalline corneal dystrophy	Uncertain significance (Jan 12, 2018)
1-11273572-T-G		not specified	Uncertain significance (Oct 27, 2022)
1-11273591-A-C		Schnyder crystalline corneal dystrophy	Likely benign (Jan 13, 2018)
1-11273625-C-T		not specified	Uncertain significance (Dec 14, 2023)
1-11273643-C-A		not specified	Uncertain significance (Nov 02, 2023)
1-11273647-A-G		Schnyder crystalline corneal dystrophy • not specified	Conflicting classifications of pathogenicity (Sep 01, 2021)
1-11273722-C-T		Schnyder crystalline corneal dystrophy	Uncertain significance (Apr 27, 2017)
1-11273755-C-T		Schnyder crystalline corneal dystrophy	Benign (Jan 15, 2024)
1-11273761-G-A		Schnyder crystalline corneal dystrophy	Likely benign (Jan 12, 2018)
1-11273808-G-A		not specified	Uncertain significance (Nov 09, 2022)
1-11273829-T-G		Schnyder crystalline corneal dystrophy	Benign/Likely benign (Aug 17, 2023)
1-11273836-A-G		Schnyder crystalline corneal dystrophy	Pathogenic (Feb 01, 2013)
1-11273866-A-G		Schnyder crystalline corneal dystrophy	Pathogenic (Aug 01, 2007)
1-11273882-T-C			Benign (Apr 16, 2022)
1-11273886-A-G		Schnyder crystalline corneal dystrophy	Pathogenic (Aug 01, 2007)
1-11273901-C-A		Schnyder crystalline corneal dystrophy	Benign (Jan 13, 2018)
1-11273948-C-T		Schnyder crystalline corneal dystrophy	Benign (Jan 13, 2018)
1-11273983-A-G		Schnyder crystalline corneal dystrophy • UBIAD1-related disorder	Benign (Feb 23, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBIAD1	protein_coding	protein_coding	ENST00000376810	2	22844

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0195	0.908	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	137	179	0.765	0.00000950	2165
Missense in Polyphen		23	47.598	0.48321		600
Synonymous	-1.89	106	84.0	1.26	0.00000494	765
Loss of Function	1.53	4	8.92	0.448	4.61e-7	102

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000970	0.0000967
Middle Eastern	0.000272	0.000272
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Metabolism of fat-soluble vitamins;Metabolism;Metabolism of vitamins and cofactors;Metabolism of vitamin K (Consensus)

Recessive Scores

• pRec: 0.189

Intolerance Scores

• loftool: 0.182
• rvis_EVS: -0.12
• rvis_percentile_EVS: 45.13

Haploinsufficiency Scores

• pHI: 0.145
• hipred: Y
• hipred_score: 0.528
• ghis: 0.615

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ubiad1
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: ubiad1
• Affected structure: blood vessel endothelial cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• 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;cellular oxidant detoxification
• Cellular component: nucleus;cytoplasm;endoplasmic reticulum;endoplasmic reticulum membrane;membrane;integral component of Golgi membrane;mitochondrial membrane
• Molecular function: prenyltransferase activity;protein binding;antioxidant activity