PLEKHJ1

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

Basic information

Region (hg38): 19:2230084-2237704

Links

ENSG00000104886 ∙ NCBI:55111 ∙ OMIM:617834 ∙ HGNC:18211 ∙ Uniprot:Q9NW61 ∙ 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 PLEKHJ1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHJ1 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in PLEKHJ1

This is a list of pathogenic ClinVar variants found in the PLEKHJ1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-2230234-C-T			Likely benign (Apr 01, 2025)
19-2230452-G-A			Likely benign (May 01, 2025)
19-2230581-G-A			Likely benign (Feb 01, 2023)
19-2233844-G-A		not specified	Uncertain significance (Feb 27, 2023)
19-2233856-C-T		not specified	Uncertain significance (Jun 03, 2022)
19-2233878-C-T		not specified	Uncertain significance (Jun 24, 2022)
19-2233887-C-T		not specified	Uncertain significance (May 17, 2023)
19-2233892-T-C		not specified	Uncertain significance (Dec 12, 2023)
19-2234015-G-A		not specified	Uncertain significance (Nov 25, 2024)
19-2234021-C-T		not specified	Uncertain significance (Jan 23, 2025)
19-2234029-T-C		not specified	Uncertain significance (Mar 01, 2025)
19-2234047-C-T		not specified	Uncertain significance (Mar 15, 2024)
19-2234050-A-G		not specified	Uncertain significance (Sep 14, 2021)
19-2234159-C-T		not specified	Uncertain significance (Aug 28, 2024)
19-2234160-G-A		not specified	Uncertain significance (Oct 24, 2024)
19-2234205-C-G		not specified	Uncertain significance (Nov 10, 2022)
19-2234209-G-C		not specified	Uncertain significance (Nov 25, 2024)
19-2234210-T-C		not specified	Uncertain significance (Aug 12, 2024)
19-2235777-C-A		not specified	Uncertain significance (Aug 05, 2024)
19-2235791-A-G		not specified	Likely benign (Nov 10, 2024)
19-2235928-C-T		not specified	Uncertain significance (Nov 17, 2023)
19-2236195-C-T		not specified	Uncertain significance (Jul 17, 2024)
19-2236198-C-G		not specified	Uncertain significance (Apr 26, 2024)
19-2236226-A-G		not specified	Uncertain significance (Aug 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHJ1	protein_coding	protein_coding	ENST00000589097	6	7702

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0653	0.877	125504	0	5	125509	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.242	88	81.8	1.08	0.00000479	951
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000588	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000365	0.0000353
Middle Eastern	0.0000588	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.115

Haploinsufficiency Scores

• pHI: 0.136
• hipred: N
• hipred_score: 0.353
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.932

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plekhj1

Gene ontology

• Biological process: receptor recycling;endosome organization;retrograde transport, endosome to Golgi
• Cellular component: early endosome;trans-Golgi network;cytosol;recycling endosome