EHBP1L1

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

Basic information

Region (hg38): 11:65576046-65592650

Links

ENSG00000173442 ∙ NCBI:254102 ∙ OMIM:619583 ∙ HGNC:30682 ∙ Uniprot:Q8N3D4 ∙ 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 EHBP1L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EHBP1L1 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				2		2
missense			100	6	1	107
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	101	8	1

Variants in EHBP1L1

This is a list of pathogenic ClinVar variants found in the EHBP1L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-65576336-G-A		not specified	Uncertain significance (Oct 11, 2024)
11-65576363-G-A		not specified	Uncertain significance (Nov 15, 2021)
11-65576377-C-G		not specified	Uncertain significance (Jun 22, 2021)
11-65579076-A-G		EHBP1L1-related disorder	Uncertain significance (Jul 02, 2024)
11-65579086-A-G		not specified	Uncertain significance (Feb 26, 2024)
11-65579109-C-T		not specified	Uncertain significance (Nov 11, 2024)
11-65579112-C-T		not specified	Uncertain significance (Jun 02, 2023)
11-65579119-G-A		not specified	Uncertain significance (Mar 29, 2023)
11-65579128-G-T		not specified	Uncertain significance (Apr 20, 2024)
11-65579348-G-T		not specified	Uncertain significance (Sep 30, 2024)
11-65579357-C-T		not specified	Uncertain significance (Mar 29, 2023)
11-65579377-C-T		not specified	Uncertain significance (Nov 28, 2023)
11-65579415-C-G		not specified	Uncertain significance (Oct 09, 2024)
11-65579427-C-G			Likely benign (Jan 01, 2023)
11-65579940-C-T		not specified	Uncertain significance (May 30, 2023)
11-65579960-G-A		not specified	Uncertain significance (Dec 03, 2024)
11-65580102-G-T		not specified	Uncertain significance (Oct 27, 2022)
11-65580112-C-T		not specified	Uncertain significance (Oct 22, 2021)
11-65580147-G-A		not specified	Uncertain significance (May 23, 2023)
11-65580150-C-T		not specified	Uncertain significance (Jun 24, 2022)
11-65580175-G-A		not specified	Uncertain significance (Nov 13, 2024)
11-65580202-T-C		not specified	Uncertain significance (Oct 27, 2021)
11-65580260-G-A		Non-immune hydrops fetalis	Likely pathogenic (Oct 09, 2024)
11-65580341-G-A		not specified	Uncertain significance (Oct 05, 2023)
11-65580459-G-A		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EHBP1L1	protein_coding	protein_coding	ENST00000309295	19	16613

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.12e-13	1.00	124729	0	41	124770	0.000164

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.846	720	787	0.915	0.0000445	9533
Missense in Polyphen		226	271.55	0.83226		3074
Synonymous	0.969	304	326	0.932	0.0000191	3275
Loss of Function	3.78	31	63.5	0.489	0.00000354	738

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000117	0.000117
Ashkenazi Jewish	0.0000997	0.0000994
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000195	0.000186
Middle Eastern	0.00	0.00
South Asian	0.000506	0.000490
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as Rab effector protein and play a role in vesicle trafficking. {ECO:0000305|PubMed:27552051}.

Recessive Scores

• pRec: 0.0889

Intolerance Scores

• loftool: 0.809
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.19

Haploinsufficiency Scores

• pHI: 0.170
• hipred: N
• hipred_score: 0.280
• ghis: 0.465

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0894

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ehbp1l1
• Phenotype: respiratory system phenotype; liver/biliary system phenotype; embryo phenotype; neoplasm; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system 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); vision/eye phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; homeostasis/metabolism phenotype; immune system phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); craniofacial phenotype; muscle phenotype

Gene ontology

• Biological process: biological_process
• Cellular component: endosome;membrane
• Molecular function: molecular_function