CTCFL

CCCTC-binding factor like, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 20:57495965-57525652

Links

ENSG00000124092 ∙ NCBI:140690 ∙ OMIM:607022 ∙ HGNC:16234 ∙ Uniprot:Q8NI51 ∙ 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 CTCFL gene.

• Inborn genetic diseases (27 variants)
• not provided (5 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTCFL 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				3	1	4
missense			27		1	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	28	3	2

Variants in CTCFL

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

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

Position	Type	Phenotype	Significance	ClinVar
20-57498563-G-A		not specified	Likely benign (Dec 11, 2023)
20-57498565-G-C		not specified	Uncertain significance (Apr 25, 2023)
20-57498585-T-C		not specified	Uncertain significance (Jun 21, 2023)
20-57498588-C-T			Benign (May 18, 2018)
20-57498603-C-T		not specified	Uncertain significance (Dec 20, 2023)
20-57498618-C-T		not specified	Uncertain significance (Aug 09, 2021)
20-57498685-C-G		not specified	Uncertain significance (Jun 29, 2023)
20-57498686-T-A		not specified	Uncertain significance (Oct 27, 2022)
20-57503443-G-A			Likely benign (Feb 01, 2023)
20-57503480-T-C		not specified	Uncertain significance (Mar 29, 2023)
20-57503526-T-C		not specified	Uncertain significance (Mar 06, 2023)
20-57503588-C-T		not specified	Uncertain significance (Feb 07, 2023)
20-57508709-C-T		not specified	Uncertain significance (Jul 09, 2021)
20-57508717-T-C			Likely benign (Nov 01, 2022)
20-57508728-A-G		not specified	Uncertain significance (Jan 30, 2024)
20-57512602-G-A		not specified	Uncertain significance (Oct 17, 2023)
20-57514630-G-A		not specified	Uncertain significance (Dec 11, 2023)
20-57514655-C-T		not specified	Uncertain significance (Mar 29, 2023)
20-57514658-C-T		not specified	Likely benign (Oct 02, 2023)
20-57514717-A-G		not specified	Uncertain significance (Mar 29, 2022)
20-57515735-G-A		See cases	Uncertain significance (Apr 21, 2023)
20-57515792-G-T		not specified	Uncertain significance (May 18, 2023)
20-57518856-C-T		not specified	Uncertain significance (Sep 17, 2021)
20-57519297-G-A		not specified	Uncertain significance (Mar 01, 2023)
20-57519356-C-T		not specified	Uncertain significance (Jun 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTCFL	protein_coding	protein_coding	ENST00000423479	11	29674

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000395	1.00	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.733	364	406	0.898	0.0000235	4626
Missense in Polyphen		82	134.11	0.61143		1438
Synonymous	-0.892	165	151	1.09	0.00000911	1275
Loss of Function	3.44	12	33.5	0.358	0.00000175	409

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000326	0.000326
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000618	0.0000615
Middle Eastern	0.000326	0.000326
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Testis-specific DNA binding protein responsible for insulator function, nuclear architecture and transcriptional control, which probably acts by recruiting epigenetic chromatin modifiers. Plays a key role in gene imprinting in male germline, by participating in the establishment of differential methylation at the IGF2/H19 imprinted control region (ICR). Directly binds the unmethylated H19 ICR and recruits the PRMT7 methyltransferase, leading to methylate histone H4 'Arg-3' to form H4R3sme2. This probably leads to recruit de novo DNA methyltransferases at these sites (By similarity). Seems to act as tumor suppressor. In association with DNMT1 and DNMT3B, involved in activation of BAG1 gene expression by binding to its promoter. Required for dimethylation of H3 lysine 4 (H3K4me2) of MYC and BRCA1 promoters. {ECO:0000250, ECO:0000269|PubMed:12011441, ECO:0000269|PubMed:18413740, ECO:0000269|PubMed:18765639}.

Recessive Scores

• pRec: 0.0912

Intolerance Scores

• loftool: 0.600
• rvis_EVS: 1.18
• rvis_percentile_EVS: 92.8

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.281

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ctcfl
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype

Gene ontology

• Biological process: regulation of gene expression by genetic imprinting;cell cycle;positive regulation of gene expression;histone methylation;DNA methylation involved in gamete generation;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;regulation of histone H3-K4 methylation
• Cellular component: nucleus;cytoplasm
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;protein binding;histone binding;sequence-specific DNA binding;transcription regulatory region DNA binding;metal ion binding