UBAP1L

ubiquitin associated protein 1 like

Basic information

Region (hg38): 15:65092760-65115200

Links

ENSG00000246922 ∙ NCBI:390595 ∙ ∙ HGNC:40028 ∙ Uniprot:F5GYI3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• inherited retinal dystrophy (Definitive), mode of inheritance: AR
• retinal degeneration (Moderate), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the UBAP1L gene.

• Retinal dystrophy (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBAP1L 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						0
missense			49	3		52
nonsense						0
start loss						0
frameshift	2					2
inframe indel						0
splice donor/acceptor (+/-2bp)	1	1				2
splice region						0
non coding	1					1
Total	4	1	49	3	0

Highest pathogenic variant AF is 0.000164

Variants in UBAP1L

This is a list of pathogenic ClinVar variants found in the UBAP1L region.

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

Position	Type	Phenotype	Significance	ClinVar
15-65093104-G-A		not specified	Uncertain significance (Oct 26, 2021)
15-65093152-A-C		not specified	Uncertain significance (Jul 19, 2023)
15-65093174-G-A		not specified	Uncertain significance (Jul 26, 2022)
15-65093180-G-C		not specified	Uncertain significance (Oct 10, 2023)
15-65093180-G-T		not specified	Uncertain significance (Aug 09, 2021)
15-65093213-G-A		not specified	Uncertain significance (Dec 19, 2023)
15-65093215-C-T		not specified	Uncertain significance (Aug 20, 2024)
15-65093216-G-A		not specified	Uncertain significance (Jan 02, 2024)
15-65094479-C-G		not specified	Uncertain significance (Dec 08, 2023)
15-65094479-C-T		not specified	Uncertain significance (Jul 13, 2022)
15-65094539-C-T		not specified	Uncertain significance (Jun 21, 2023)
15-65094548-C-T		not specified	Uncertain significance (Mar 17, 2023)
15-65094564-G-C		not specified	Uncertain significance (Feb 28, 2024)
15-65094583-C-T		Retinal dystrophy	Pathogenic (Apr 15, 2024)
15-65099554-C-T		not specified	Uncertain significance (Jan 07, 2022)
15-65099598-C-A		not specified	Uncertain significance (May 25, 2022)
15-65099656-G-T		not specified	Uncertain significance (Jul 22, 2024)
15-65099703-CG-C		Retinal dystrophy	Pathogenic (Apr 15, 2024)
15-65099711-G-A		not specified	Uncertain significance (Jan 07, 2022)
15-65102117-G-C		not specified	Uncertain significance (Apr 28, 2022)
15-65102134-G-T		not specified	Likely benign (Mar 29, 2022)
15-65102143-G-A		not specified	Uncertain significance (Mar 07, 2024)
15-65102152-G-A		not specified	Uncertain significance (May 18, 2023)
15-65102153-T-C		not specified	Uncertain significance (Oct 06, 2021)
15-65102156-A-G		not specified	Uncertain significance (Oct 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBAP1L	protein_coding	protein_coding	ENST00000559089	5	22198

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00600	0.914	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.740	128	154	0.832	0.00000934	2388
Missense in Polyphen		43	57.11	0.75293		893
Synonymous	0.870	60	69.2	0.867	0.00000453	848
Loss of Function	1.50	5	10.2	0.492	5.19e-7	140

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ubap1l

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
• Cellular component: ESCRT I complex
• Molecular function: ubiquitin binding