GCFC2

GC-rich sequence DNA-binding factor 2

Basic information

Region (hg38): 2:75652000-75710985

Previous symbols: [ "TCF9", "C2orf3" ]

Links

ENSG00000005436 ∙ NCBI:6936 ∙ OMIM:189901 ∙ HGNC:1317 ∙ Uniprot:P16383 ∙ 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 GCFC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GCFC2 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				1		1
missense			48	3	1	52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	4	1

Variants in GCFC2

This is a list of pathogenic ClinVar variants found in the GCFC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-75652236-C-T		not specified	Uncertain significance (Dec 03, 2021)
2-75652255-A-G		not specified	Uncertain significance (Oct 25, 2022)
2-75652257-G-A		not specified	Uncertain significance (Aug 03, 2022)
2-75652531-C-G		not specified	Uncertain significance (Jun 29, 2023)
2-75652537-G-A		not specified	Uncertain significance (Mar 24, 2023)
2-75654804-C-T		not specified	Uncertain significance (Jun 17, 2024)
2-75654860-T-C			Likely benign (Oct 01, 2022)
2-75655055-C-A			Likely benign (Dec 31, 2019)
2-75655055-C-T			Likely benign (Apr 09, 2018)
2-75655100-C-T		not specified	Uncertain significance (May 02, 2024)
2-75655122-A-G		not specified	Uncertain significance (Oct 08, 2024)
2-75655161-A-T		not specified	Uncertain significance (Jan 05, 2022)
2-75655218-G-A		not specified	Uncertain significance (Sep 17, 2021)
2-75655228-T-A		not specified	Uncertain significance (Nov 17, 2022)
2-75655239-T-G		not specified	Uncertain significance (Nov 09, 2024)
2-75655269-C-T		not specified	Uncertain significance (Dec 03, 2024)
2-75655278-G-A		not specified	Likely benign (Nov 15, 2023)
2-75664678-A-C		not specified	Uncertain significance (Sep 20, 2023)
2-75664757-A-G		not specified	Uncertain significance (Mar 05, 2024)
2-75665954-G-A		not specified	Uncertain significance (Apr 24, 2023)
2-75666009-C-T		not specified	Uncertain significance (Aug 26, 2024)
2-75670170-G-A		not specified	Uncertain significance (Jul 07, 2024)
2-75670172-G-A		not specified	Likely benign (May 07, 2024)
2-75670175-G-T		not specified	Uncertain significance (Mar 16, 2022)
2-75670202-C-T		not specified	Uncertain significance (Oct 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GCFC2	protein_coding	protein_coding	ENST00000321027	17	58990

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.56e-24	0.00315	125470	2	276	125748	0.00111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00392	377	377	0.999	0.0000178	5115
Missense in Polyphen		94	100.66	0.93386		1388
Synonymous	-1.49	154	132	1.16	0.00000624	1398
Loss of Function	0.655	39	43.7	0.893	0.00000228	543

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00215	0.00212
Ashkenazi Jewish	0.000842	0.000695
East Asian	0.00146	0.00141
Finnish	0.0000473	0.0000462
European (Non-Finnish)	0.00114	0.00109
Middle Eastern	0.00146	0.00141
South Asian	0.00231	0.00206
Other	0.000709	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Factor that represses transcription. It binds to the GC- rich sequences (5'-GCGGGGC-3') present in the epidermal growth factor receptor, beta-actin, and calcium-dependent protease promoters. Involved in pre-mRNA splicing through regulating spliceosome C complex formation. May play a role during late-stage splicing events and turnover of excised inrons. {ECO:0000269|PubMed:24304693}.

Recessive Scores

• pRec: 0.189

Intolerance Scores

• rvis_EVS: 1.51
• rvis_percentile_EVS: 95.47

Haploinsufficiency Scores

• pHI: 0.0801
• hipred: N
• hipred_score: 0.146
• ghis: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• 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: Gcfc2

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;spliceosomal complex assembly;mRNA splicing, via spliceosome;regulation of transcription, DNA-templated;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;nucleoplasm;nucleolus;cytosol;U2-type post-mRNA release spliceosomal complex
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription repressor activity, RNA polymerase II-specific;protein binding