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 (260 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	3		4
missense			259	12		271
nonsense			1			1
start loss						0
frameshift			3			3
splice donor/acceptor (+/-2bp)		1	3			4
Total	0	1	267	15	0

Highest pathogenic variant AF is 0.0000061600886

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
		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

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

Gene ontology

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