EHD1

EH domain containing 1, the group of EF-hand domain containing

Basic information

Region (hg38): 11:64851642-64888296

Previous symbols: [ "PAST1" ]

Links

ENSG00000110047 ∙ NCBI:10938 ∙ OMIM:605888 ∙ HGNC:3242 ∙ Uniprot:Q9H4M9 ∙ 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 EHD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EHD1 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				5	4	9
missense			30			30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					3	3
Total	0	0	30	5	7

Variants in EHD1

This is a list of pathogenic ClinVar variants found in the EHD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-64854362-C-A		not specified	Uncertain significance (Nov 21, 2022)
11-64854454-A-C		not specified	Uncertain significance (May 06, 2024)
11-64854470-C-T		not specified	Uncertain significance (Feb 23, 2023)
11-64854501-G-A			Likely benign (Jul 31, 2018)
11-64854545-C-T		not specified	Uncertain significance (Jun 10, 2022)
11-64854546-G-A			Benign (Jun 10, 2018)
11-64854571-G-T		not specified	Uncertain significance (Apr 20, 2024)
11-64854601-G-A		not specified	Uncertain significance (Jun 11, 2021)
11-64854630-G-A			Likely benign (Feb 12, 2018)
11-64854636-G-A			Likely benign (Mar 30, 2018)
11-64854647-C-T		not specified	Uncertain significance (Jan 31, 2022)
11-64854676-G-A		not specified	Uncertain significance (Aug 04, 2023)
11-64854730-A-G		not specified	Uncertain significance (Jun 21, 2023)
11-64854734-A-T		not specified	Uncertain significance (Dec 11, 2023)
11-64854740-C-T		not specified	Uncertain significance (Feb 12, 2024)
11-64854745-C-T		not specified	Uncertain significance (Jan 31, 2022)
11-64854770-T-C		not specified	Uncertain significance (Mar 02, 2023)
11-64854773-C-T		not specified	Uncertain significance (Jan 22, 2024)
11-64854819-C-T			Likely benign (Jun 22, 2018)
11-64854820-G-A		not specified	Uncertain significance (Dec 21, 2023)
11-64855313-C-T			Benign (Dec 31, 2019)
11-64855333-G-A		not specified	Uncertain significance (Oct 05, 2023)
11-64855371-C-T		not specified	Uncertain significance (Mar 01, 2023)
11-64855395-C-A		not specified	Uncertain significance (Jul 05, 2023)
11-64855397-G-G			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EHD1	protein_coding	protein_coding	ENST00000320631	5	36655

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.983	0.0166	125713	0	23	125736	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.10	238	348	0.684	0.0000226	3520
Missense in Polyphen		48	102.75	0.46716		1080
Synonymous	-0.0697	167	166	1.01	0.0000130	1062
Loss of Function	3.58	1	16.9	0.0593	8.16e-7	191

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000185	0.000185
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: ATP- and membrane-binding protein that controls membrane reorganization/tubulation upon ATP hydrolysis. In vitro causes vesiculation of endocytic membranes (PubMed:24019528). Acts in early endocytic membrane fusion and membrane trafficking of recycling endosomes (PubMed:15020713, PubMed:17233914, PubMed:20801876). Recruited to endosomal membranes upon nerve growth factor stimulation, indirectly regulates neurite outgrowth (By similarity). Plays a role in myoblast fusion (By similarity). 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 (CV), an early step in cilium biogenesis. Proposed to be required for the fusion of distal appendage vesicles (DAVs) to form the CV by recruiting SNARE complex component SNAP29. Is required for recruitment of transition zone proteins CEP290, RPGRIP1L, TMEM67 and B9D2, and of IFT20 following DAV reorganization before Rab8- dependent ciliary membrane extension. Required for the loss of CCP110 form the mother centriole essential for the maturation of the basal body during ciliogenesis (PubMed:25686250). {ECO:0000250|UniProtKB:Q641Z6, ECO:0000250|UniProtKB:Q9WVK4, ECO:0000269|PubMed:15020713, ECO:0000269|PubMed:17233914, ECO:0000269|PubMed:20801876, ECO:0000269|PubMed:24019528, ECO:0000269|PubMed:25686250}.
• Pathway: Endocytosis - Homo sapiens (human);Insulin Signaling;Factors involved in megakaryocyte development and platelet production;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.163

Intolerance Scores

• loftool: 0.257
• rvis_EVS: -1.38
• rvis_percentile_EVS: 4.39

Haploinsufficiency Scores

• pHI: 0.191
• hipred: Y
• hipred_score: 0.685
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.956

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ehd1
• 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; reproductive system phenotype; hematopoietic system phenotype; skeleton phenotype; vision/eye phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; craniofacial phenotype

Gene ontology

• Biological process: intracellular protein transport;endocytosis;blood coagulation;positive regulation of cholesterol storage;neuron projection development;endocytic recycling;low-density lipoprotein particle clearance;cholesterol homeostasis;protein homooligomerization;cilium assembly;protein localization to cilium;positive regulation of myoblast fusion;cellular response to nerve growth factor stimulus;positive regulation of endocytic recycling
• Cellular component: lipid droplet;plasma membrane;endosome membrane;membrane;ciliary pocket membrane;platelet dense tubular network membrane;early endosome membrane;recycling endosome membrane;extracellular exosome
• Molecular function: calcium ion binding;protein binding;ATP binding;GTP binding;Rab GTPase binding;identical protein binding;cadherin binding