EHD2

EH domain containing 2, the group of EF-hand domain containing

Basic information

Region (hg38): 19:47713422-47743134

Previous symbols: [ "PAST2" ]

Links

ENSG00000024422 ∙ NCBI:30846 ∙ OMIM:605890 ∙ HGNC:3243 ∙ Uniprot:Q9NZN4 ∙ 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 EHD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EHD2 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			44			44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	0	0

Variants in EHD2

This is a list of pathogenic ClinVar variants found in the EHD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-47716643-C-T		not specified	Uncertain significance (May 31, 2023)
19-47716655-C-T		not specified	Uncertain significance (Sep 17, 2021)
19-47716671-C-T		not specified	Uncertain significance (Dec 20, 2023)
19-47716680-C-T		not specified	Uncertain significance (Oct 25, 2024)
19-47716700-C-T		not specified	Uncertain significance (Oct 12, 2022)
19-47716734-G-A		not specified	Uncertain significance (Apr 07, 2023)
19-47716785-A-C		not specified	Uncertain significance (Feb 06, 2024)
19-47716874-G-A		not specified	Uncertain significance (Nov 08, 2024)
19-47716910-G-A		not specified	Uncertain significance (Dec 28, 2023)
19-47716957-C-T		not specified	Likely benign (Feb 22, 2025)
19-47716965-C-T		not specified	Uncertain significance (Feb 24, 2025)
19-47716980-G-A		not specified	Uncertain significance (Aug 13, 2021)
19-47716997-G-A		not specified	Uncertain significance (Dec 06, 2022)
19-47718531-A-G		not specified	Uncertain significance (Mar 29, 2024)
19-47718573-A-G		not specified	Uncertain significance (Sep 12, 2024)
19-47718574-T-C		not specified	Uncertain significance (Dec 05, 2022)
19-47718604-G-A		not specified	Uncertain significance (Jan 31, 2025)
19-47725922-G-C		not specified	Uncertain significance (Jul 26, 2024)
19-47725934-G-A		not specified	Uncertain significance (Apr 20, 2023)
19-47726018-A-T		not specified	Uncertain significance (Jun 28, 2024)
19-47726037-T-C		not specified	Uncertain significance (Jun 25, 2024)
19-47726126-C-G		not specified	Uncertain significance (Jan 27, 2025)
19-47726135-C-G		not specified	Uncertain significance (Apr 01, 2024)
19-47736375-G-A		not specified	Uncertain significance (Apr 23, 2024)
19-47736391-A-G		not specified	Uncertain significance (Apr 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EHD2	protein_coding	protein_coding	ENST00000263277	5	29792

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.308	0.692	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.88	269	371	0.725	0.0000264	3495
Missense in Polyphen		54	95.706	0.56423		940
Synonymous	0.500	171	180	0.953	0.0000148	1101
Loss of Function	2.92	4	17.0	0.235	7.85e-7	200

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000879	0.0000879
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000906	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000332	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: ATP- and membrane-binding protein that controls membrane reorganization/tubulation upon ATP hydrolysis (By similarity). Plays a role in membrane trafficking between the plasma membrane and endosomes (PubMed:17233914). Important for the internalization of GLUT4. Required for fusion of myoblasts to skeletal muscle myotubes. Required for normal translocation of FER1L5 to the plasma membrane (By similarity). Regulates the equilibrium between cell surface-associated and cell surface-dissociated caveolae by constraining caveolae at the cell membrane (PubMed:25588833). {ECO:0000250|UniProtKB:Q8BH64, ECO:0000269|PubMed:17233914, ECO:0000269|PubMed:25588833}.
• Pathway: Endocytosis - Homo sapiens (human);Insulin Signaling;Factors involved in megakaryocyte development and platelet production;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.0710
• rvis_EVS: -1.04
• rvis_percentile_EVS: 7.77

Haploinsufficiency Scores

• pHI: 0.149
• hipred: Y
• hipred_score: 0.662
• ghis: 0.659

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.913

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ehd2

Gene ontology

• Biological process: endocytosis;blood coagulation;cortical actin cytoskeleton organization;endocytic recycling;protein localization to plasma membrane;plasma membrane tubulation;positive regulation of myoblast fusion;positive regulation of endocytic recycling
• Cellular component: nucleus;cytosol;plasma membrane;caveola;endosome membrane;microtubule cytoskeleton;extrinsic component of membrane;intercellular bridge;perinuclear region of cytoplasm;recycling endosome membrane;extracellular exosome
• Molecular function: nucleic acid binding;calcium ion binding;protein binding;ATP binding;GTP binding;hydrolase activity;protein domain specific binding;identical protein binding