JMJD1C
Basic information
Region (hg38): 10:63167221-63521850
Previous symbols: [ "TRIP8" ]
Links
Phenotypes
GenCC
Source:
- complex neurodevelopmental disorder (Limited), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (3 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 | 310 | 23 | 341 | |||
missense | 771 | 27 | 13 | 812 | ||
nonsense | 5 | |||||
start loss | 0 | |||||
frameshift | 6 | |||||
inframe indel | 21 | 24 | ||||
splice donor/acceptor (+/-2bp) | 2 | |||||
splice region | 1 | 21 | 16 | 5 | 43 | |
non coding | 70 | 14 | 90 | |||
Total | 3 | 1 | 816 | 407 | 53 |
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 • not specified | Uncertain significance (May 29, 2024) | ||
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:
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:
- 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