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.

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			30	2		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	2	0

Variants in EHD4

This is a list of pathogenic ClinVar variants found in the EHD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-41900728-G-A		not specified	Uncertain significance (Oct 13, 2023)
15-41900737-T-C		not specified	Uncertain significance (Nov 08, 2022)
15-41900829-T-C		not specified	Uncertain significance (Jan 05, 2022)
15-41900859-T-C		not specified	Uncertain significance (Jul 06, 2022)
15-41900864-G-C		not specified	Uncertain significance (Nov 13, 2023)
15-41900887-T-C		not specified	Uncertain significance (May 12, 2024)
15-41900895-G-C		not specified	Uncertain significance (May 15, 2024)
15-41900911-G-C		not specified	Uncertain significance (Feb 06, 2023)
15-41900941-C-A		not specified	Uncertain significance (Dec 07, 2021)
15-41900941-C-T		not specified	Uncertain significance (Mar 04, 2024)
15-41900962-C-T		not specified	Uncertain significance (May 07, 2024)
15-41901007-C-T		not specified	Uncertain significance (Jan 18, 2023)
15-41901051-G-A		not specified	Likely benign (Nov 18, 2023)
15-41901057-G-A		not specified	Likely benign (Dec 19, 2022)
15-41909720-G-T		not specified	Uncertain significance (Aug 01, 2022)
15-41919277-T-C		not specified	Uncertain significance (Feb 23, 2023)
15-41919308-C-T		not specified	Uncertain significance (Mar 01, 2023)
15-41919320-G-A		not specified	Uncertain significance (Dec 20, 2023)
15-41919373-C-T		not specified	Uncertain significance (Mar 16, 2022)
15-41919386-G-T		not specified	Uncertain significance (Apr 26, 2024)
15-41919427-T-C		not specified	Uncertain significance (Jun 12, 2023)
15-41919476-C-T		not specified	Uncertain significance (Dec 26, 2023)
15-41919491-C-T		not specified	Uncertain significance (Feb 01, 2023)
15-41919503-G-A		not specified	Uncertain significance (Nov 13, 2023)
15-41919523-G-A		not specified	Uncertain significance (Aug 16, 2021)

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