CHTOP

chromatin target of PRMT1, the group of Transcription and export complex 1 subunits

Basic information

Region (hg38): 1:153633982-153646306

Previous symbols: [ "C1orf77" ]

Links

ENSG00000160679

∙ NCBI:26097 ∙ OMIM:614206 ∙ HGNC:24511 ∙ Uniprot:Q9Y3Y2 ∙ 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 CHTOP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHTOP 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			17 clinvar	1 clinvar		18
nonsense						0
start loss						0
frameshift						0
inframe indel				1 clinvar		1
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	17	2	0

Variants in CHTOP

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

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

Position	Phenotype	Significance	ClinVar
1-153636608-C-T	not specified	Uncertain significance (Sep 27, 2024)	3492834
1-153638295-C-G	not specified	Likely benign (Nov 10, 2024)	3492836
1-153638327-C-T	not specified	Likely benign (Aug 16, 2021)	2364505
1-153642256-A-G	not specified	Uncertain significance (Nov 13, 2024)	3492837
1-153642324-A-G	not specified	Uncertain significance (Aug 20, 2024)	2352568
1-153642331-G-A	not specified	Uncertain significance (Nov 21, 2023)	3144856
1-153642337-G-C	not specified	Uncertain significance (Mar 03, 2022)	2277945
1-153642355-G-A	not specified	Uncertain significance (Nov 09, 2023)	3144857
1-153642364-C-G	not specified	Uncertain significance (Jul 05, 2024)	3492835
1-153642397-G-C	not specified	Uncertain significance (May 24, 2024)	3267292
1-153642403-T-C	not specified	Uncertain significance (Jul 30, 2023)	2598779
1-153643329-G-A	not specified	Uncertain significance (Feb 28, 2023)	2470658
1-153643349-G-A	not specified	Uncertain significance (Apr 04, 2023)	2532770
1-153645069-G-A	not specified	Uncertain significance (Feb 28, 2023)	2472814
1-153645072-A-T	not specified	Uncertain significance (Sep 17, 2021)	2251666
1-153645099-G-GGAGGCC		Likely benign (Feb 01, 2024)	3025635
1-153645106-G-T	not specified	Uncertain significance (Jun 25, 2024)	3492833
1-153645112-G-A	not specified	Uncertain significance (Dec 26, 2023)	3144859
1-153645145-G-A	not specified	Uncertain significance (May 24, 2023)	2563293
1-153645147-C-T	not specified	Uncertain significance (Jan 07, 2025)	3833356
1-153645195-T-A	not specified	Uncertain significance (Aug 30, 2022)	2309595

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHTOP	protein_coding	protein_coding	ENST00000368694	5	12258

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.764	0.236	125736	0	3	125739	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.70	105	167	0.630	0.0000110	1536
Missense in Polyphen		0	0.48393	0		4
Synonymous	0.138	60	61.4	0.978	0.00000360	567
Loss of Function	3.27	3	17.9	0.167	0.00000155	136

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	0.0000462	0.0000462
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Plays an important role in the ligand-dependent activation of estrogen receptor target genes (PubMed:19858291). May play a role in the silencing of fetal globin genes (PubMed:20688955). Recruits the 5FMC complex to ZNF148, leading to desumoylation of ZNF148 and subsequent transactivation of ZNF148 target genes (By similarity). Plays an important role in the tumorigenicity of glioblastoma cells. Binds to 5- hydroxymethylcytosine (5hmC) and associates with the methylosome complex containing PRMT1, PRMT5, MEP50 and ERH. The CHTOP- methylosome complex associated with 5hmC is recruited to selective sites on the chromosome, where it methylates H4R3 and activates the transcription of genes involved in glioblastomagenesis (PubMed:25284789). {ECO:0000250|UniProtKB:Q9CY57, ECO:0000269|PubMed:19858291, ECO:0000269|PubMed:20688955, ECO:0000269|PubMed:25284789}.;
Pathway: Gene expression (Transcription);RNA Polymerase II Transcription;Metabolism of RNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;Transport of Mature mRNA derived from an Intron-Containing Transcript;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

pRec: 0.107

Intolerance Scores

loftool
rvis_EVS: -0.18
rvis_percentile_EVS: 39.95

Haploinsufficiency Scores

pHI: 0.320
hipred: Y
hipred_score: 0.686
ghis: 0.623

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: E
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: Chtop
Phenotype: homeostasis/metabolism phenotype; muscle phenotype; craniofacial phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; respiratory system phenotype; immune system phenotype; renal/urinary system phenotype; skeleton phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; vision/eye 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); 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); embryo phenotype;

Gene ontology

Biological process: RNA export from nucleus;mRNA export from nucleus;positive regulation of cell population proliferation;positive regulation of histone methylation;mRNA 3'-end processing;positive regulation of ATPase activity;positive regulation of helicase activity
Cellular component: transcription export complex;nucleoplasm;nucleolus;nuclear speck;cytoplasmic ribonucleoprotein granule
Molecular function: RNA binding;protein binding;methyl-CpG binding