GTF2H2C

GTF2H2 family member C

Basic information

Region (hg38): 5:69560191-69595221

Links

ENSG00000183474 ∙ NCBI:728340 ∙ ∙ HGNC:31394 ∙ Uniprot:Q6P1K8 ∙ 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 GTF2H2C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTF2H2C 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTF2H2C	protein_coding	protein_coding	ENST00000510979	15	34516

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0219	0.916	125496	0	55	125551	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.853	49	68.9	0.711	0.00000327	2573
Missense in Polyphen		16	18.807	0.85074		804
Synonymous	1.20	15	22.2	0.676	0.00000115	713
Loss of Function	1.59	4	9.20	0.435	4.29e-7	330

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00295	0.00281
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000607	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000286	0.0000265
Middle Eastern	0.0000607	0.0000544
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the core-TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. {ECO:0000250}.
• Pathway: Nucleotide excision repair - Homo sapiens (human);Basal transcription factors - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.109

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.380
• ghis: 0.412

Essentials

• essential_gene_CRISPR: E
• 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

Gene ontology

• Biological process: nucleotide-excision repair;transcription, DNA-templated;regulation of transcription by RNA polymerase II
• Cellular component: transcription factor TFIIH core complex;transcription factor TFIIH holo complex;nuclear speck
• Molecular function: nucleic acid binding;protein binding;zinc ion binding