JMJD1C

jumonji domain containing 1C, the group of Lysine demethylases|MicroRNA protein coding host genes

Basic information

Region (hg38): 10:63167220-63521850

Previous symbols: [ "TRIP8" ]

Links

ENSG00000171988 ∙ NCBI:221037 ∙ OMIM:604503 ∙ HGNC:12313 ∙ Uniprot:Q15652 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the JMJD1C gene.

• Early myoclonic encephalopathy (1131 variants)
• not provided (70 variants)
• Inborn genetic diseases (70 variants)
• JMJD1C-related condition (7 variants)
• not specified (5 variants)
• JMJD1C-associated Neurodevelopmental Disorder (5 variants)
• Neurodevelopmental disorder (2 variants)
• See cases (2 variants)
• Benign familial infantile epilepsy (1 variants)
• TELO2-related intellectual disability-neurodevelopmental disorder (1 variants)
• JMJD1C-related Neurodevelopmental disorder (1 variants)
• Hepatoblastoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JMJD1C 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			8	282	23	313
missense		1	691	29	13	734
nonsense			4			4
start loss						0
frameshift	3		3			6
inframe indel			16		3	19
splice donor/acceptor (+/-2bp)			2			2
splice region		1	17	14	6	38
non coding			5	59	15	79
Total	3	1	729	370	54

Variants in JMJD1C

This is a list of pathogenic ClinVar variants found in the JMJD1C region.

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

Position	Type	Phenotype	Significance	ClinVar
10-63168034-CTG-C		JMJD1C-related disorder	Likely benign (Jul 10, 2019)
10-63168047-A-C		Early myoclonic encephalopathy	Uncertain significance (Oct 13, 2022)
10-63168048-A-G		Early myoclonic encephalopathy	Likely benign (Sep 01, 2020)
10-63168056-C-G		Early myoclonic encephalopathy	Uncertain significance (Jul 24, 2019)
10-63168063-C-G		Early myoclonic encephalopathy	Benign (Feb 01, 2024)
10-63168068-C-G		Early myoclonic encephalopathy	Uncertain significance (Jun 16, 2020)
10-63168074-C-A		Early myoclonic encephalopathy	Uncertain significance (Jun 04, 2022)
10-63168075-C-T		Early myoclonic encephalopathy	Benign (Dec 22, 2023)
10-63168077-C-T		Early myoclonic encephalopathy • JMJD1C-related disorder	Likely benign (Jan 27, 2024)
10-63168078-G-A		Early myoclonic encephalopathy • JMJD1C-related disorder	Likely benign (Dec 12, 2023)
10-63168080-G-T		Early myoclonic encephalopathy	Uncertain significance (Jan 01, 2023)
10-63168082-ATCT-A		Early myoclonic encephalopathy	Uncertain significance (Oct 16, 2023)
10-63168092-C-G			Uncertain significance (Apr 19, 2023)
10-63168134-C-T		Early myoclonic encephalopathy	Uncertain significance (Oct 04, 2022)
10-63168143-G-T		Early myoclonic encephalopathy	Likely benign (Jul 29, 2020)
10-63168145-TG-T		Early myoclonic encephalopathy	Likely benign (May 15, 2023)
10-63168146-G-A		Early myoclonic encephalopathy	Likely benign (Apr 06, 2023)
10-63168148-T-C		Early myoclonic encephalopathy	Likely benign (Dec 08, 2023)
10-63168150-A-G		Early myoclonic encephalopathy	Likely benign (Nov 27, 2023)
10-63168418-G-A		Early myoclonic encephalopathy	Likely benign (Nov 25, 2021)
10-63168431-T-C		Early myoclonic encephalopathy	Uncertain significance (Mar 09, 2021)
10-63168432-T-C		Early myoclonic encephalopathy	Uncertain significance (Dec 18, 2023)
10-63168448-T-A		Early myoclonic encephalopathy	Uncertain significance (Dec 18, 2021)
10-63168450-A-G		Early myoclonic encephalopathy	Likely benign (Dec 11, 2023)
10-63168459-T-G		Early myoclonic encephalopathy	Uncertain significance (Apr 01, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JMJD1C	protein_coding	protein_coding	ENST00000399262	26	298742

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	7.95e-16	124790	0	11	124801	0.0000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	1138	1.29e+3	0.881	0.0000630	16782
Missense in Polyphen		270	478.95	0.56373		6199
Synonymous	-1.81	495	446	1.11	0.0000214	4741
Loss of Function	9.35	3	108	0.0278	0.00000544	1415

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000895	0.0000895
Ashkenazi Jewish	0.0000996	0.0000993
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000279	0.0000265
Middle Eastern	0.0000556	0.0000556
South Asian	0.00	0.00
Other	0.000500	0.000495

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role in histone code. Demethylation of Lys residue generates formaldehyde and succinate. May be involved in hormone-dependent transcriptional activation, by participating in recruitment to androgen-receptor target genes (By similarity). {ECO:0000250}.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human);Pathways Affected in Adenoid Cystic Carcinoma;Factors involved in megakaryocyte development and platelet production;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.0285
• rvis_EVS: -0.55
• rvis_percentile_EVS: 19.81

Haploinsufficiency Scores

• pHI: 0.789
• hipred: Y
• hipred_score: 0.518
• ghis: 0.605

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.836

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Jmjd1c
• Phenotype: cellular phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); endocrine/exocrine gland phenotype; vision/eye phenotype; skeleton phenotype; reproductive system phenotype

Zebrafish Information Network

• Gene name: jmjd1cb
• Affected structure: myeloid cell development
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: regulation of transcription, DNA-templated;blood coagulation;histone H3-K9 demethylation;oxidation-reduction process
• Cellular component: chromatin;nucleus;nucleoplasm
• Molecular function: transcription regulatory region sequence-specific DNA binding;protein binding;chromatin DNA binding;histone demethylase activity (H3-K9 specific);metal ion binding;thyroid hormone receptor binding;dioxygenase activity