JMJD8

jumonji domain containing 8

Basic information

Region (hg38): 16:681669-684528

Previous symbols: [ "C16orf20" ]

Links

ENSG00000161999 ∙ NCBI:339123 ∙ ∙ HGNC:14148 ∙ Uniprot:Q96S16 ∙ 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 JMJD8 gene.

• not provided (59 variants)
• Inborn genetic diseases (33 variants)
• Spinocerebellar ataxia 48 (15 variants)
• Autosomal recessive spinocerebellar ataxia 16 (11 variants)
• Autosomal recessive spinocerebellar ataxia 16;Spinocerebellar ataxia 48 (1 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JMJD8 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			31	1		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	7	14	26	23	7	77
Total	7	14	57	24	7

Highest pathogenic variant AF is 0.0000156

Variants in JMJD8

This is a list of pathogenic ClinVar variants found in the JMJD8 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-681725-T-G			Benign (Sep 25, 2019)
16-681771-C-T			Benign (May 15, 2021)
16-681774-G-A			Likely benign (Jul 25, 2023)
16-681776-T-C			Likely benign (Aug 16, 2023)
16-681785-A-G		Autosomal recessive spinocerebellar ataxia 16	Uncertain significance (Jul 12, 2021)
16-681789-C-T			Likely benign (Nov 08, 2022)
16-681792-G-A		Spinocerebellar ataxia 48	Likely pathogenic (Mar 07, 2022)
16-681803-G-A		not specified	Uncertain significance (Jan 03, 2024)
16-681807-G-A			Uncertain significance (Feb 08, 2022)
16-681811-G-A			Likely benign (Jan 02, 2024)
16-681811-G-T			Uncertain significance (Sep 07, 2023)
16-681812-C-T			Likely pathogenic (May 16, 2019)
16-681813-G-A			Uncertain significance (Jan 12, 2024)
16-681820-C-T			Likely benign (Sep 01, 2023)
16-681821-G-A		Inborn genetic diseases • Spinocerebellar ataxia 48	Uncertain significance (Aug 30, 2023)
16-681836-G-A		not specified	Conflicting classifications of pathogenicity (Feb 20, 2024)
16-681843-A-G		Inborn genetic diseases	Likely benign (Feb 27, 2023)
16-681845-G-A			Uncertain significance (Jun 20, 2023)
16-681849-G-A		Inborn genetic diseases	Uncertain significance (Nov 07, 2023)
16-681855-A-G			Likely benign (Dec 02, 2022)
16-681859-G-C			Uncertain significance (Oct 19, 2022)
16-681876-AGCACGTGAGGGTGCCCCCCACCCACATGTGGGTCTGTGTGTGT-A		Autosomal recessive spinocerebellar ataxia 16	Uncertain significance (Aug 01, 2021)
16-681886-GG-TT			Uncertain significance (May 23, 2023)
16-681889-G-GC			Benign (Dec 15, 2023)
16-681891-C-G		Autosomal recessive spinocerebellar ataxia 16	Uncertain significance (Jun 21, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JMJD8	protein_coding	protein_coding	ENST00000412368	9	2859

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.06e-14	0.00428	124521	0	37	124558	0.000149

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.92	224	156	1.43	0.00000914	1741
Missense in Polyphen		74	62.365	1.1866		629
Synonymous	-3.61	107	68.9	1.55	0.00000419	590
Loss of Function	-0.954	18	14.1	1.27	6.03e-7	172

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000520	0.000469
Ashkenazi Jewish	0.000299	0.000298
East Asian	0.000169	0.000167
Finnish	0.00	0.00
European (Non-Finnish)	0.000172	0.000168
Middle Eastern	0.000169	0.000167
South Asian	0.0000654	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a positive regulator of TNF-induced NF- kappa-B signaling (PubMed:27671354). Regulates angiogenesis and cellular metabolism through interaction with PKM (PubMed:27199445). {ECO:0000269|PubMed:27199445, ECO:0000269|PubMed:27671354}.

Intolerance Scores

• loftool: 0.579
• rvis_EVS: 0.88
• rvis_percentile_EVS: 89.07

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.204
• ghis: 0.429

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.235

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Jmjd8
• Phenotype: cellular phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of glycolytic process;positive regulation of I-kappaB kinase/NF-kappaB signaling;regulation of pyruvate kinase activity;positive regulation of sprouting angiogenesis
• Cellular component: nucleus;cytoplasm;endoplasmic reticulum;endoplasmic reticulum lumen
• Molecular function: protein binding