JPT1

Jupiter microtubule associated homolog 1

Basic information

Region (hg38): 17:75135248-75168281

Previous symbols: [ "HN1" ]

Links

ENSG00000189159 ∙ NCBI:51155 ∙ OMIM:619242 ∙ HGNC:14569 ∙ Uniprot:Q9UK76 ∙ 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 JPT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JPT1 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			11			11
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in JPT1

This is a list of pathogenic ClinVar variants found in the JPT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-75136011-C-G		not specified	Uncertain significance (Jan 03, 2022)
17-75136099-G-A		not specified	Uncertain significance (May 05, 2022)
17-75136160-G-A		not specified	Uncertain significance (Dec 06, 2022)
17-75136222-G-A		not specified	Uncertain significance (May 16, 2023)
17-75136245-C-A		not specified	Uncertain significance (Jun 07, 2023)
17-75147561-G-T		not specified	Uncertain significance (May 11, 2022)
17-75147576-C-T		not specified	Uncertain significance (Apr 12, 2022)
17-75147584-G-C		not specified	Uncertain significance (Aug 06, 2021)
17-75147590-G-A		not specified	Uncertain significance (Jun 17, 2024)
17-75147642-T-C		not specified	Uncertain significance (May 27, 2022)
17-75148540-G-A		not specified	Uncertain significance (Feb 01, 2023)
17-75148588-A-G		not specified	Uncertain significance (Apr 18, 2023)
17-75148663-C-T		not specified	Uncertain significance (Mar 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JPT1	protein_coding	protein_coding	ENST00000356033	4	33034

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00250	0.796	125704	0	42	125746	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.598	84	101	0.833	0.00000556	1169
Missense in Polyphen		22	35.595	0.61806		468
Synonymous	1.05	30	38.3	0.784	0.00000201	363
Loss of Function	1.03	5	8.19	0.610	3.47e-7	100

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000980	0.0000967
Middle Eastern	0.000218	0.000217
South Asian	0.000882	0.000882
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Modulates negatively AKT-mediated GSK3B signaling (PubMed:21323578, PubMed:22155408). Induces CTNNB1 'Ser-33' phosphorylation and degradation through the suppression of the inhibitory 'Ser-9' phosphorylation of GSK3B, which represses the function of the APC:CTNNB1:GSK3B complex and the interaction with CDH1/E-cadherin in adherent junctions (PubMed:25169422). Plays a role in the regulation of cell cycle and cell adhesion (PubMed:25169422, PubMed:25450365). Has an inhibitory role on AR- signaling pathway through the induction of receptor proteosomal degradation (PubMed:22155408). {ECO:0000269|PubMed:21323578, ECO:0000269|PubMed:22155408, ECO:0000269|PubMed:25169422, ECO:0000269|PubMed:25450365}.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.58

Haploinsufficiency Scores

• pHI: 0.398
• hipred: N
• hipred_score: 0.184
• ghis: 0.515

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Jpt1

Gene ontology

• Cellular component: nucleus;nucleolus;cytoplasm;nuclear membrane