EHD3

EH domain containing 3, the group of EF-hand domain containing

Basic information

Region (hg38): 2:31234152-31269451

Previous symbols: [ "PAST3" ]

Links

ENSG00000013016 ∙ NCBI:30845 ∙ OMIM:605891 ∙ HGNC:3244 ∙ Uniprot:Q9NZN3 ∙ 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 EHD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EHD3 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			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	27	0	3

Variants in EHD3

This is a list of pathogenic ClinVar variants found in the EHD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-31234637-G-T		not specified	Uncertain significance (Feb 21, 2024)
2-31234655-A-G		not specified	Uncertain significance (Sep 16, 2021)
2-31234711-G-C		not specified	Uncertain significance (Apr 22, 2022)
2-31234713-G-C		not specified	Likely benign (Mar 30, 2024)
2-31234742-C-A		not specified	Uncertain significance (Mar 30, 2024)
2-31234743-G-A		not specified	Uncertain significance (Mar 30, 2024)
2-31234796-C-T		not specified	Uncertain significance (Jun 03, 2024)
2-31244339-T-A		not specified	Uncertain significance (Sep 17, 2021)
2-31249477-C-T			Benign (May 08, 2018)
2-31260519-T-C		not specified	Uncertain significance (Aug 09, 2021)
2-31260652-A-G			Benign (May 08, 2018)
2-31260787-C-G		not specified	Uncertain significance (Oct 26, 2022)
2-31260856-G-T		not specified	Uncertain significance (May 23, 2024)
2-31260876-C-T		not specified	Uncertain significance (Feb 14, 2023)
2-31261588-C-T		not specified	Uncertain significance (May 29, 2024)
2-31261600-G-A		not specified	Uncertain significance (Feb 28, 2023)
2-31261611-C-G		not specified	Uncertain significance (Nov 09, 2023)
2-31261618-A-C		not specified	Uncertain significance (Mar 29, 2023)
2-31261663-C-T		not specified	Uncertain significance (Dec 27, 2023)
2-31266202-G-C		not specified	Uncertain significance (Mar 29, 2024)
2-31266206-G-C		not specified	Uncertain significance (Oct 14, 2023)
2-31266258-C-T		not specified	Uncertain significance (Jun 29, 2023)
2-31266265-T-C		not specified	Uncertain significance (Aug 02, 2022)
2-31266307-G-A		not specified	Uncertain significance (Mar 03, 2022)
2-31266333-G-T		not specified	Uncertain significance (Nov 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EHD3	protein_coding	protein_coding	ENST00000322054	6	35434

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0422	0.957	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.82	241	335	0.720	0.0000200	3552
Missense in Polyphen		55	90.023	0.61095		992
Synonymous	0.0789	148	149	0.992	0.0000101	1053
Loss of Function	2.86	6	19.7	0.305	0.00000101	216

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000231	0.000231
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000881	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: ATP- and membrane-binding protein that controls membrane reorganization/tubulation upon ATP hydrolysis (PubMed:25686250). In vitro causes tubulation of endocytic membranes (PubMed:24019528). Binding to phosphatidic acid induces its membrane tubulation activity (By similarity). Plays a role in endocytic transport. Involved in early endosome to recycling endosome compartment (ERC), retrograde early endosome to Golgi, and endosome to plasma membrane (rapid recycling) protein transport. Involved in the regulation of Golgi maintenance and morphology (PubMed:16251358, PubMed:17233914, PubMed:19139087, PubMed:23781025). Involved in the recycling of internalized D1 dopamine receptor (PubMed:21791287). Plays a role in cardiac protein trafficking probably implicating ANK2 (PubMed:20489164). Involved in the ventricular membrane targeting of SLC8A1 and CACNA1C and probably the atrial membrane localization of CACNA1GG and CACNA1H implicated in the regulation of atrial myocyte excitability and cardiac conduction (By similarity). In conjunction with EHD4 may be involved in endocytic trafficking of KDR/VEGFR2 implicated in control of glomerular function (By similarity). Involved in the rapid recycling of integrin beta-3 implicated in cell adhesion maintenance (PubMed:23781025). Involved in the unidirectional retrograde dendritic transport of endocytosed BACE1 and in efficient sorting of BACE1 to axons implicating a function in neuronal APP processing (By similarity). Plays a role in the formation of the ciliary vesicle, an early step in cilium biogenesis; possibly sharing redundant functions with EHD1 (PubMed:25686250). {ECO:0000250|UniProtKB:Q9QXY6, ECO:0000269|PubMed:16251358, ECO:0000269|PubMed:17233914, ECO:0000269|PubMed:19139087, ECO:0000269|PubMed:21791287, ECO:0000269|PubMed:23781025, ECO:0000269|PubMed:24019528, ECO:0000269|PubMed:25686250, ECO:0000305|PubMed:20489164}.
• Pathway: Endocytosis - Homo sapiens (human);Factors involved in megakaryocyte development and platelet production;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.139
• rvis_EVS: -1.13
• rvis_percentile_EVS: 6.48

Haploinsufficiency Scores

• pHI: 0.158
• hipred: Y
• hipred_score: 0.672
• ghis: 0.585

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.891

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ehd3
• Phenotype: homeostasis/metabolism phenotype; cellular 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); growth/size/body region 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); normal phenotype; renal/urinary system phenotype

Zebrafish Information Network

• Gene name: ehd3
• Affected structure: neuromast hair cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: receptor recycling;blood coagulation;protein transport;endocytic recycling;early endosome to Golgi transport;protein homooligomerization;regulation of cardiac muscle contraction;cilium assembly;protein localization to plasma membrane;regulation of cardiac muscle cell membrane potential;Golgi to lysosome transport;positive regulation of voltage-gated calcium channel activity;regulation of Golgi organization;regulation of cardiac conduction
• Cellular component: nucleus;cytoplasm;cytosol;focal adhesion;endosome membrane;ciliary pocket membrane;endocytic vesicle;myelin sheath;perinuclear region of cytoplasm;recycling endosome membrane
• Molecular function: nucleic acid binding;calcium ion binding;protein binding;ATP binding;GTP binding