JMJD1C

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

Basic information

Region (hg38): 10:63167221-63521850

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
neurodevelopmental disorder (Limited), mode of inheritance: AD
22q11.2 deletion syndrome (Supportive), mode of inheritance: AD

ClinVar

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

not provided (2 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. These statistics are base on trasncript: . Only rare variants are included in the table.

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			7 clinvar	315 clinvar	23 clinvar	345
missense		1 clinvar	799 clinvar	27 clinvar	13 clinvar	840
nonsense			5 clinvar			5
start loss						0
frameshift	2 clinvar		3 clinvar			5
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	2	1	815	342	36

Loading clinvar variants...

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