UBAP1

ubiquitin associated protein 1, the group of ESCRT-I

Basic information

Region (hg38): 9:34179004-34252523

Previous symbols: [ "UBAP" ]

Links

ENSG00000165006 ∙ NCBI:51271 ∙ OMIM:609787 ∙ HGNC:12461 ∙ Uniprot:Q9NZ09 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown
• hereditary spastic paraplegia 12 (Supportive), mode of inheritance: AD
• spastic paraplegia 80, autosomal dominant (Strong), mode of inheritance: AD
• spastic paraplegia 80, autosomal dominant (Strong), mode of inheritance: AD
• spastic paraplegia 80, autosomal dominant (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spastic paraplegia 80, autosomal dominant	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	Neurologic	30929741; 31203368

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the UBAP1 gene.

• Spastic paraplegia 80, autosomal dominant (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBAP1 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		1
missense		1	18	3	2	24
nonsense	1					1
start loss						0
frameshift	2		1			3
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	1		2
non coding			4	1	3	8
Total	3	1	23	5	5

Variants in UBAP1

This is a list of pathogenic ClinVar variants found in the UBAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-34179039-A-T		Inborn genetic diseases • UBAP1-related disorder	Conflicting classifications of pathogenicity (Mar 11, 2024)
9-34179067-G-T		Inborn genetic diseases	Uncertain significance (Nov 14, 2023)
9-34179074-C-T			Likely benign (Mar 01, 2022)
9-34179081-G-T		Inborn genetic diseases	Uncertain significance (Oct 04, 2022)
9-34179102-G-T		Inborn genetic diseases	Uncertain significance (May 07, 2024)
9-34179144-C-G		Inborn genetic diseases	Uncertain significance (Apr 01, 2024)
9-34179187-C-T		Inborn genetic diseases	Uncertain significance (Jun 26, 2023)
9-34179202-C-T		Inborn genetic diseases	Uncertain significance (Jun 02, 2023)
9-34220857-G-A			Benign (May 17, 2021)
9-34234285-G-T		Inborn genetic diseases	Uncertain significance (Feb 28, 2023)
9-34234314-T-G			Uncertain significance (Jun 20, 2022)
9-34241227-G-C		Inborn genetic diseases	Uncertain significance (Feb 27, 2024)
9-34241251-G-A			Likely benign (May 01, 2024)
9-34241272-A-AGTGAATTC		Spastic paraplegia 80, autosomal dominant	Pathogenic (Sep 10, 2019)
9-34241276-C-T		Inborn genetic diseases	Uncertain significance (Apr 01, 2024)
9-34241294-T-C		Inborn genetic diseases	Uncertain significance (Jun 30, 2023)
9-34241310-C-CCCAGA		Spastic paraplegia 80, autosomal dominant	Pathogenic (May 10, 2019)
9-34241312-C-T		Inborn genetic diseases	Uncertain significance (Aug 02, 2023)
9-34241315-AG-A		Spastic paraplegia 80, autosomal dominant	Pathogenic (May 04, 2022)
9-34241319-C-CG		Spastic paraplegia 80, autosomal dominant	Pathogenic (May 10, 2019)
9-34241329-A-T		Spastic paraplegia 80, autosomal dominant	Uncertain significance (Jul 06, 2023)
9-34241341-A-T		Spastic paraplegia 80, autosomal dominant	Pathogenic (Aug 09, 2019)
9-34241351-G-A		Inborn genetic diseases	Uncertain significance (Jun 29, 2023)
9-34241384-T-TC		Spastic paraplegia 80, autosomal dominant	Pathogenic (May 10, 2019)
9-34241393-G-A		Inborn genetic diseases	Uncertain significance (Nov 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBAP1	protein_coding	protein_coding	ENST00000545103	6	73519

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.912	0.0883	125743	0	2	125745	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.869	240	281	0.854	0.0000142	3720
Missense in Polyphen		65	85.526	0.76		1236
Synonymous	0.111	107	108	0.986	0.00000584	1105
Loss of Function	3.32	2	16.6	0.120	6.98e-7	257

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	0.0000462	0.0000462
European (Non-Finnish)	0.00000884	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the ESCRT-I complex, a regulator of vesicular trafficking process. Binds to ubiquitinated cargo proteins and is required for the sorting of endocytic ubiquitinated cargos into multivesicular bodies (MVBs). Plays a role in the proteasomal degradation of ubiquitinated cell-surface proteins, such as EGFR and BST2. {ECO:0000269|PubMed:21757351, ECO:0000269|PubMed:22405001}.
• Pathway: Disease;Vesicle-mediated transport;Membrane Trafficking;Assembly Of The HIV Virion;Budding and maturation of HIV virion;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;Endosomal Sorting Complex Required For Transport (ESCRT);Infectious disease;Membrane binding and targetting of GAG proteins;Synthesis And Processing Of GAG, GAGPOL Polyproteins (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.68

Haploinsufficiency Scores

• pHI: 0.404
• hipred: N
• hipred_score: 0.387
• ghis: 0.583

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00979

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ubap1

Gene ontology

• Biological process: protein transport;endosomal transport;viral life cycle;ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
• Cellular component: ESCRT I complex;cytoplasm;Golgi apparatus;cytosol;plasma membrane;endosome membrane
• Molecular function: protein binding;ubiquitin binding