EHBP1

EH domain binding protein 1, the group of NT-C2 domain containing

Basic information

Region (hg38): 2:62673851-63046487

Links

ENSG00000115504 ∙ NCBI:23301 ∙ OMIM:609922 ∙ HGNC:29144 ∙ Uniprot:Q8NDI1 ∙ 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 EHBP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EHBP1 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				4	1	5
missense			70	10	1	81
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	70	14	2

Variants in EHBP1

This is a list of pathogenic ClinVar variants found in the EHBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-62707273-A-G		not specified	Uncertain significance (May 31, 2023)
2-62707274-T-C		not specified	Uncertain significance (Oct 26, 2022)
2-62747391-G-C			Benign (Mar 28, 2018)
2-62747417-G-A		not specified	Uncertain significance (Jul 30, 2023)
2-62764336-T-C		not specified	Uncertain significance (Jul 19, 2022)
2-62771346-A-G		not specified	Uncertain significance (Mar 01, 2023)
2-62771376-C-T		not specified	Uncertain significance (Nov 21, 2023)
2-62771387-G-C		not specified	Uncertain significance (Aug 02, 2021)
2-62826114-C-G		not specified	Uncertain significance (Apr 20, 2023)
2-62826120-A-T		not specified	Uncertain significance (Sep 07, 2022)
2-62826214-C-G		not specified	Uncertain significance (Aug 05, 2023)
2-62826219-G-A		not specified	Likely benign (Mar 23, 2022)
2-62831091-C-T		EHBP1-related disorder	Likely benign (Apr 30, 2019)
2-62831106-A-G		EHBP1-related disorder	Benign (Jun 30, 2019)
2-62831106-AGAT-A			Uncertain significance (-)
2-62831109-T-A		not specified	Likely benign (Dec 06, 2021)
2-62831118-G-C		not specified	Uncertain significance (Jan 06, 2023)
2-62831120-A-G		not specified	Uncertain significance (Aug 26, 2022)
2-62831121-C-G		not specified	Uncertain significance (Nov 18, 2022)
2-62858481-G-A		not specified	Uncertain significance (Mar 12, 2024)
2-62859208-A-C		not specified	Uncertain significance (Jul 14, 2023)
2-62859208-A-G		not specified	Uncertain significance (Dec 14, 2023)
2-62859231-A-T		not specified	Uncertain significance (May 14, 2024)
2-62859244-A-G		not specified	Uncertain significance (May 17, 2023)
2-62864733-C-T		not specified	Uncertain significance (Mar 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EHBP1	protein_coding	protein_coding	ENST00000263991	24	372637

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.307	0.693	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.19	550	634	0.868	0.0000329	8096
Missense in Polyphen		187	276.91	0.67531		3486
Synonymous	0.651	211	223	0.945	0.0000114	2232
Loss of Function	5.98	16	69.9	0.229	0.00000411	841

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000621	0.0000615
Ashkenazi Jewish	0.000113	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000151	0.000149
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000990	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in actin reorganization. Links clathrin- mediated endocytosis to the actin cytoskeleton. May act as Rab effector protein and play a role in vesicle trafficking (PubMed:14676205, PubMed:27552051). Required for perinuclear sorting and insulin-regulated recycling of SLC2A4/GLUT4 in adipocytes (By similarity). {ECO:0000250|UniProtKB:Q69ZW3, ECO:0000269|PubMed:14676205, ECO:0000305|PubMed:27552051}.
• Disease: DISEASE: Prostate cancer, hereditary, 12 (HPC12) [MIM:611868]: A condition associated with familial predisposition to cancer of the prostate. Most prostate cancers are adenocarcinomas that develop in the acini of the prostatic ducts. Other rare histopathologic types of prostate cancer that occur in approximately 5% of patients include small cell carcinoma, mucinous carcinoma, prostatic ductal carcinoma, transitional cell carcinoma, squamous cell carcinoma, basal cell carcinoma, adenoid cystic carcinoma (basaloid), signet-ring cell carcinoma and neuroendocrine carcinoma. {ECO:0000269|PubMed:18264098}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.529
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.22

Haploinsufficiency Scores

• pHI: 0.243
• hipred: N
• hipred_score: 0.474
• ghis: 0.536

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.935

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ehbp1

Gene ontology

• Biological process: endocytosis;protein transport
• Cellular component: endosome;cytosol;plasma membrane