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.

not_specified (232 variants)
not_provided (7 variants)
EHBP1L1-related_disorder (4 variants)
Non-immune_hydrops_fetalis (3 variants)

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. These statistics are base on transcript: NM_001099409.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar		3
missense			225 clinvar	11 clinvar		236
nonsense						0
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)		1 clinvar	2 clinvar			3
Total	0	1	229	14	0

Highest pathogenic variant AF is 0.0000061600886

Loading clinvar variants...

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