TAF1C

TATA-box binding protein associated factor, RNA polymerase I subunit C

Basic information

Region (hg38): 16:84177847-84187070

Links

ENSG00000103168 ∙ NCBI:9013 ∙ OMIM:604905 ∙ HGNC:11534 ∙ Uniprot:Q15572 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TAF1C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAF1C 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				2	2	4
missense			81	11	2	94
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			2	3	3	8
Total	0	0	85	16	7

Variants in TAF1C

This is a list of pathogenic ClinVar variants found in the TAF1C region.

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

Position	Type	Phenotype	Significance	ClinVar
16-84177857-T-C		Primary ciliary dyskinesia 13	Uncertain significance (Jan 12, 2018)
16-84177859-T-C		not specified • Primary ciliary dyskinesia 13	Benign/Likely benign (Nov 22, 2023)
16-84177877-C-T		not specified • Primary ciliary dyskinesia 13	Benign (Jul 30, 2021)
16-84177882-ATGTC-A		Primary ciliary dyskinesia	Uncertain significance (Jun 14, 2016)
16-84177908-T-C		Primary ciliary dyskinesia 13	Likely benign (Jan 12, 2018)
16-84178112-C-T			Benign (Nov 12, 2018)
16-84178129-A-C			Benign (Nov 12, 2018)
16-84178966-C-T		not specified	Uncertain significance (Jan 02, 2024)
16-84178993-G-A		not specified	Uncertain significance (Mar 04, 2024)
16-84179001-C-G		not specified	Uncertain significance (Apr 12, 2024)
16-84179011-C-T		not specified	Uncertain significance (Oct 17, 2023)
16-84179020-C-A		not specified	Uncertain significance (Oct 31, 2022)
16-84179021-G-A		not specified	Likely benign (Jun 13, 2022)
16-84179024-C-A		not specified	Uncertain significance (Jun 10, 2024)
16-84179026-C-G		not specified	Uncertain significance (Mar 08, 2024)
16-84179039-A-G		not specified	Uncertain significance (Apr 25, 2022)
16-84179086-A-G		not specified	Uncertain significance (Jul 20, 2021)
16-84179111-T-C		not specified	Uncertain significance (Jul 09, 2021)
16-84179116-C-T		not specified	Likely benign (Aug 17, 2021)
16-84179132-C-G		not specified	Uncertain significance (Mar 31, 2024)
16-84179159-A-T		not specified	Uncertain significance (Jun 27, 2022)
16-84179184-G-A			Likely benign (Oct 01, 2023)
16-84179186-G-A		not specified	Likely benign (Oct 31, 2022)
16-84179197-G-A		not specified	Uncertain significance (Jan 23, 2023)
16-84179200-T-C		not specified	Uncertain significance (Apr 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TAF1C	protein_coding	protein_coding	ENST00000567759	13	9212

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.46e-24	0.000610	125673	0	73	125746	0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.29	684	535	1.28	0.0000356	5397
Missense in Polyphen		222	202.41	1.0968		2221
Synonymous	-3.89	312	236	1.32	0.0000154	1938
Loss of Function	0.112	37	37.7	0.980	0.00000212	354

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000991	0.000972
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000170	0.000163
Finnish	0.000141	0.000139
European (Non-Finnish)	0.000270	0.000255
Middle Eastern	0.000170	0.000163
South Asian	0.000394	0.000392
Other	0.000858	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. The rate of PIC formation probably is primarily dependent on the rate of association of SL1/TIF-IB with the rDNA promoter. SL1/TIF-IB is involved in stabilization of nucleolar transcription factor 1/UBTF on rDNA. Formation of SL1/TIF-IB excludes the association of TBP with TFIID subunits. Recruits RNA polymerase I to the rRNA gene promoter via interaction with RRN3. {ECO:0000269|PubMed:11250903, ECO:0000269|PubMed:15970593}.
• Pathway: B-WICH complex positively regulates rRNA expression;Positive epigenetic regulation of rRNA expression;SIRT1 negatively regulates rRNA expression;NoRC negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription);RNA Polymerase I Promoter Clearance;RNA Polymerase I Transcription Termination;RNA Polymerase I Transcription;RNA Polymerase I Transcription Initiation;RNA Polymerase I Promoter Escape;RNA Polymerase I Chain Elongation (Consensus)

Recessive Scores

• pRec: 0.0925

Intolerance Scores

• rvis_EVS: 0.59
• rvis_percentile_EVS: 82.46

Haploinsufficiency Scores

• pHI: 0.242
• hipred: N
• hipred_score: 0.146
• ghis: 0.504

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.656

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Taf1c

Gene ontology

• Biological process: RNA polymerase I preinitiation complex assembly;regulation of transcription by RNA polymerase I;transcription by RNA polymerase I;transcription initiation from RNA polymerase I promoter;termination of RNA polymerase I transcription;transcription by RNA polymerase II;positive regulation of gene expression, epigenetic
• Cellular component: fibrillar center;nucleus;nucleoplasm;nucleolus
• Molecular function: RNA polymerase I CORE element sequence-specific DNA binding;protein binding