JPT2

Jupiter microtubule associated homolog 2

Basic information

Region (hg38): 16:1678256-1702280

Previous symbols: [ "C16orf34", "HN1L" ]

Links

ENSG00000206053 ∙ NCBI:90861 ∙ OMIM:619241 ∙ HGNC:14137 ∙ Uniprot:Q9H910 ∙ 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 JPT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JPT2 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			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in JPT2

This is a list of pathogenic ClinVar variants found in the JPT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-1678322-G-C		not specified	Uncertain significance (Apr 07, 2022)
16-1678326-C-A		not specified	Uncertain significance (Jul 14, 2023)
16-1678326-C-G		not specified	Uncertain significance (Dec 13, 2023)
16-1678331-A-G		not specified	Uncertain significance (Feb 28, 2024)
16-1678333-C-G		not specified	Uncertain significance (Aug 02, 2021)
16-1678334-G-A		not specified	Uncertain significance (Feb 06, 2023)
16-1678337-G-A		not specified	Uncertain significance (Sep 23, 2023)
16-1678347-C-G		not specified	Uncertain significance (Sep 01, 2021)
16-1685465-C-T		not specified	Uncertain significance (Apr 23, 2024)
16-1685559-G-C		not specified	Uncertain significance (May 09, 2023)
16-1685576-C-T		not specified	Uncertain significance (Apr 25, 2023)
16-1691843-G-C		not specified	Uncertain significance (Aug 11, 2022)
16-1691881-G-A		not specified	Uncertain significance (Feb 22, 2023)
16-1691923-A-T		not specified	Uncertain significance (Mar 06, 2023)
16-1698826-C-T		not specified	Uncertain significance (May 30, 2024)
16-1698840-C-G		not specified	Uncertain significance (Dec 12, 2023)
16-1698858-G-A		not specified	Likely benign (Mar 21, 2022)
16-1698897-C-T		not specified	Uncertain significance (Oct 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JPT2	protein_coding	protein_coding	ENST00000248098	5	24025

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.233	0.737	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.448	98	111	0.881	0.00000635	1230
Missense in Polyphen		36	43.999	0.8182		469
Synonymous	0.854	35	42.0	0.833	0.00000274	379
Loss of Function	1.81	2	7.29	0.274	3.73e-7	95

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.100

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• pHI: 0.268
• hipred: N
• hipred_score: 0.345
• ghis: 0.555

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Jpt2

Gene ontology

• Cellular component: nucleus;cytosol;plasma membrane