JRKL

JRK like, the group of DNA transposon derived genes|Helix-turn-helix CENPB type domain containing

Basic information

Region (hg38): 11:96389989-96507574

Links

ENSG00000183340 ∙ NCBI:8690 ∙ OMIM:603211 ∙ HGNC:6200 ∙ Uniprot:Q9Y4A0 ∙ 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 JRKL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JRKL 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			16
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	0	0

Variants in JRKL

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

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

Position	Type	Phenotype	Significance	ClinVar
11-96390867-C-T		not specified	Uncertain significance (Mar 01, 2023)
11-96391019-G-A		not specified	Uncertain significance (Jun 29, 2022)
11-96391042-G-T		not specified	Uncertain significance (Dec 22, 2023)
11-96391052-A-G		not specified	Uncertain significance (Nov 29, 2023)
11-96391056-G-A		not specified	Uncertain significance (May 02, 2024)
11-96391062-T-G		not specified	Uncertain significance (Jul 11, 2023)
11-96391095-A-T		not specified	Uncertain significance (Sep 26, 2023)
11-96391181-G-A		not specified	Uncertain significance (Jan 10, 2023)
11-96391232-G-A		not specified	Uncertain significance (Apr 19, 2023)
11-96391562-T-A		not specified	Uncertain significance (Nov 07, 2023)
11-96391633-G-C		not specified	Uncertain significance (May 20, 2024)
11-96391869-T-A		not specified	Uncertain significance (Dec 27, 2023)
11-96391932-T-G		not specified	Uncertain significance (Oct 20, 2021)
11-96392048-G-A		not specified	Uncertain significance (Oct 26, 2021)
11-96392063-C-G		not specified	Uncertain significance (May 15, 2023)
11-96392142-T-A		not specified	Uncertain significance (Jan 04, 2024)
11-96392163-T-C		not specified	Uncertain significance (Feb 27, 2023)
11-96392202-A-T		not specified	Uncertain significance (Nov 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JRKL	protein_coding	protein_coding	ENST00000458427	1	117586

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000200	0.979	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.74	195	277	0.705	0.0000138	3457
Missense in Polyphen		56	107.27	0.52206		1304
Synonymous	-0.0407	97	96.5	1.01	0.00000465	994
Loss of Function	2.05	9	18.5	0.486	0.00000109	232

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.472
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.31

Haploinsufficiency Scores

• pHI: 0.205
• hipred: N
• hipred_score: 0.483
• ghis: 0.663

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Jrkl

Gene ontology

• Biological process: central nervous system development
• Cellular component: nucleus
• Molecular function: DNA binding