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.

• not_specified (85 variants)
• not_provided (2 variants)

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. These statistics are base on transcript: NM_000003203.5. 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			77	8	1	86
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	77	9	1

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