USHBP1

USH1 protein network component harmonin binding protein 1

Basic information

Region (hg38): 19:17249171-17282786

Links

ENSG00000130307 ∙ NCBI:83878 ∙ OMIM:611810 ∙ HGNC:24058 ∙ Uniprot:Q8N6Y0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the USHBP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USHBP1 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			56	4		60
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	56	4	0

Variants in USHBP1

This is a list of pathogenic ClinVar variants found in the USHBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-17250244-A-G		not specified	Likely benign (May 01, 2022)
19-17250254-G-T		not specified	Uncertain significance (May 17, 2023)
19-17250256-G-A		not specified	Uncertain significance (Feb 13, 2023)
19-17250260-G-A		not specified	Uncertain significance (May 26, 2024)
19-17250280-A-G		not specified	Uncertain significance (Jun 29, 2023)
19-17250280-A-T		not specified	Uncertain significance (Mar 31, 2023)
19-17250299-C-T		not specified	Uncertain significance (Nov 07, 2022)
19-17250376-T-C		not specified	Uncertain significance (Jun 17, 2022)
19-17250394-C-T		not specified	Uncertain significance (Apr 07, 2022)
19-17250414-G-A		not specified	Likely benign (May 30, 2023)
19-17251595-A-G		not specified	Uncertain significance (Oct 18, 2021)
19-17251613-C-G		not specified	Uncertain significance (Oct 16, 2023)
19-17251613-C-T		not specified	Uncertain significance (Nov 03, 2023)
19-17251618-C-T		not specified	Uncertain significance (May 08, 2024)
19-17251628-G-A		not specified	Uncertain significance (May 21, 2024)
19-17251636-C-T		not specified	Uncertain significance (Jan 08, 2024)
19-17251938-G-A		not specified	Uncertain significance (Nov 30, 2022)
19-17255416-C-T		not specified	Uncertain significance (May 31, 2022)
19-17255424-G-T		not specified	Uncertain significance (Jan 23, 2023)
19-17255468-C-T		not specified	Uncertain significance (May 18, 2023)
19-17255473-C-G		not specified	Uncertain significance (Nov 12, 2021)
19-17255524-C-T		not specified	Uncertain significance (Jan 31, 2022)
19-17255540-G-A		not specified	Uncertain significance (Nov 07, 2023)
19-17255564-G-A		not specified	Uncertain significance (Feb 27, 2023)
19-17255570-C-T		not specified	Uncertain significance (Aug 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USHBP1	protein_coding	protein_coding	ENST00000252597	12	33611

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.00e-17	0.120	125559	1	188	125748	0.000752

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.162	439	430	1.02	0.0000265	4481
Missense in Polyphen		84	79.911	1.0512		975
Synonymous	0.688	158	169	0.933	0.00000951	1501
Loss of Function	1.17	30	37.8	0.794	0.00000250	338

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00236	0.00226
Ashkenazi Jewish	0.00140	0.00139
East Asian	0.000387	0.000381
Finnish	0.000187	0.000185
European (Non-Finnish)	0.000629	0.000624
Middle Eastern	0.000387	0.000381
South Asian	0.000985	0.000948
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.972
• rvis_EVS: -0.39
• rvis_percentile_EVS: 27.06

Haploinsufficiency Scores

• pHI: 0.0504
• hipred: N
• hipred_score: 0.123
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.190

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ushbp1
• Phenotype: skeleton phenotype; homeostasis/metabolism phenotype

Gene ontology

• Molecular function: protein binding;PDZ domain binding