PLEKHJ1

protein-coding

pleckstrin homology domain containing J1, the group of Pleckstrin homology domain containing|MicroRNA protein coding host genes

Gene summary

Predicted to be involved in endosome organization; receptor recycling; and retrograde transport, endosome to Golgi. Predicted to be located in Golgi apparatus; clathrin-coated vesicle; and cytosol. Predicted to be active in early endosome; recycling endosome; and trans-Golgi network. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_018049.3

Inheritance

—

ClinVar variants

U:43B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr19:2,230,084-2,237,704

External References & Databases

Ensembl (ENSG00000104886)

Transcript & Mutation Effects

hg38 • Region Span ~7.6 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 PLEKHJ1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 40

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018049.3. 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						0
missense			40 clinvar	2 clinvar		42
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	43	2	0	45

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 42 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018049.3	RefSeq	NP_060519.1	6	MANE Select
ENST00000326631.7	Ensembl	ENSP00000318075.2	6	MANE Select
NM_001300836.3	RefSeq	NP_001287765.1	6	Standard
ENST00000586608.3	Ensembl	ENSP00000464924.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

receptor recycling
endosome organization
retrograde transport, endosome to Golgi

Cellular Component

early endosome
trans-Golgi network
cytosol
recycling endosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000589097
Coding exons: 6
Length: 7702
Individuals with no LoFs: 125504
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125509
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.242	88	81.8	1.08	0.00000479	951
Missense (PolyPhen)		26	26.152	0.99418		332
Synonymous	-0.341	36	33.5	1.07	0.00000215	275
Loss of Function	1.60	3	7.83	0.383	3.32e-7	101

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000059	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000037	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.115

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Indispensability pred.: E
Indispensability score: 0.932

Gene Damage Prediction

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