ENTHD1

protein-coding

ENTH domain containing 1

Gene summary

Predicted to enable clathrin binding activity and phospholipid binding activity. Predicted to be involved in endocytosis. Predicted to be located in cytoplasm. Predicted to be part of clathrin vesicle coat. Predicted to be active in endosome and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_152512.4

Inheritance

—

ClinVar variants

U:67B:19

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr22:39,743,044-39,893,864

External References & Databases

Ensembl (ENSG00000176177)

Transcript & Mutation Effects

hg38 • Region Span ~150.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ENTHD1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 82

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152512.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			66 clinvar	17 clinvar		83
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	67	19	0	86

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152512.4	RefSeq	NP_689725.2	6	MANE Select
ENST00000325157.7	Ensembl	ENSP00000317431.6	6	MANE Select
XM_006724149.4	RefSeq	XP_006724212.1	6	Standard
XM_006724150.4	RefSeq	XP_006724213.1	6	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000325157
Coding exons: 6
Length: 150820
Individuals with no LoFs: 124509
Homozygous LoFs: 1
Heterozygous LoFs: 1236
Defined: 125746
p: 0.00493

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.329	296	312	0.948	0.0000151	3988
Missense (PolyPhen)		66	79.635	0.82878		1045
Synonymous	1.32	100	118	0.846	0.00000595	1178
Loss of Function	1.37	13	19.6	0.665	9.05e-7	271

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0017	0.0017	notable
Latino/Admixed American	0.0010	0.0010	notable
Ashkenazi Jewish	0.00060	0.00060	rare
East Asian	0.00078	0.00076	rare
Finnish	0.010	0.010	notable
European (Non-Finnish)	0.0075	0.0076	notable
South Asian	0.0018	0.0018	notable
Other	0.0046	0.0046	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0765

Intolerance Scores

LoFtool: 0.941
RVIS EVS: -0.16
RVIS percentile EVS: 42.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.135

Gene Damage Prediction

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