EHD4

EH domain containing 4, the group of EF-hand domain containing

Basic information

Region (hg38): 15:41895933-41972557

Previous symbols: [ "PAST4" ]

Links

ENSG00000103966

∙ NCBI:30844 ∙ OMIM:605892 ∙ HGNC:3245 ∙ Uniprot:Q9H223 ∙ 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 EHD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EHD4 gene is commonly pathogenic or not. These statistics are base on transcript: . 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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			45 clinvar	2 clinvar		47
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	45	2	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EHD4	protein_coding	protein_coding	ENST00000220325	6	73827

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000419	0.992	125696	0	52	125748	0.000207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.55	262	343	0.764	0.0000209	3551
Missense in Polyphen		125	180.16	0.69384		1873
Synonymous	0.597	154	164	0.941	0.0000120	1055
Loss of Function	2.34	11	23.1	0.476	0.00000130	236

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000827	0.000826
Ashkenazi Jewish	0.00	0.00
East Asian	0.000367	0.000326
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000987	0.0000967
Middle Eastern	0.000367	0.000326
South Asian	0.000196	0.000196
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: ATP- and membrane-binding protein that probably controls membrane reorganization/tubulation upon ATP hydrolysis. Plays a role in early endosomal transport. {ECO:0000269|PubMed:17233914, ECO:0000269|PubMed:18331452}.;
Pathway: Endocytosis - Homo sapiens (human);Neurotrophic factor-mediated Trk receptor signaling (Consensus)

Recessive Scores

pRec: 0.122

Intolerance Scores

loftool: 0.280
rvis_EVS: -0.75
rvis_percentile_EVS: 13.58

Haploinsufficiency Scores

pHI: 0.187
hipred: Y
hipred_score: 0.543
ghis: 0.578

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.702

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ehd4
Phenotype: homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; renal/urinary system phenotype; 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); reproductive 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);

Gene ontology

Biological process: pinocytosis;regulation of endocytosis;endocytic recycling;positive regulation of peptidyl-tyrosine phosphorylation;protein homooligomerization;cellular response to growth factor stimulus
Cellular component: nucleus;endoplasmic reticulum;plasma membrane;membrane;early endosome membrane;perinuclear region of cytoplasm;recycling endosome membrane;extracellular exosome
Molecular function: nucleic acid binding;calcium ion binding;protein binding;ATP binding;GTP binding;cadherin binding