TAF13

TATA-box binding protein associated factor 13, the group of General transcription factor IID complex subunits

Basic information

Region (hg38): 1:109062496-109076012

Previous symbols: [ "TAF2K" ]

Links

ENSG00000197780 ∙ NCBI:6884 ∙ OMIM:600774 ∙ HGNC:11546 ∙ Uniprot:Q15543 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive primary microcephaly (Supportive), mode of inheritance: AR
• intellectual disability, autosomal recessive 60 (Limited), mode of inheritance: AR
• intellectual disability, autosomal recessive 60 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, autosomal recessive 60	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Endocrine; Neurologic	28257693

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TAF13 gene.

• Intellectual disability, autosomal recessive 60 (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAF13 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
missense	2		4			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region						0
non coding				1	1	2
Total	2	1	4	3	1

Variants in TAF13

This is a list of pathogenic ClinVar variants found in the TAF13 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-109064662-C-A		not specified	Uncertain significance (Oct 26, 2022)
1-109066134-C-A		Intellectual disability, autosomal recessive 60	Likely pathogenic (Jan 14, 2021)
1-109066143-T-C		not specified	Uncertain significance (Mar 15, 2024)
1-109066173-T-C		not specified	Uncertain significance (Nov 09, 2023)
1-109066189-A-G			Likely benign (Jun 14, 2018)
1-109066214-C-T		Inborn genetic diseases	Uncertain significance (Feb 26, 2018)
1-109066217-T-C		Intellectual disability, autosomal recessive 60	Uncertain significance (Jun 19, 2019)
1-109066220-A-T		Intellectual disability, autosomal recessive 60	Pathogenic (Mar 02, 2017)
1-109074995-G-GA		not specified	Uncertain significance (Apr 09, 2024)
1-109075001-A-T		Intellectual disability, autosomal recessive 60	Pathogenic (Mar 02, 2017)
1-109075045-T-A		not specified	Uncertain significance (May 15, 2024)
1-109075911-G-C		TAF13-related disorder	Likely benign (May 10, 2019)
1-109075933-T-C		TAF13-related disorder	Likely benign (Jun 01, 2024)
1-109075949-C-T		Intellectual disability, autosomal recessive 60	Benign (Nov 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TAF13	protein_coding	protein_coding	ENST00000338366	4	13517

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0159	0.892	125721	0	25	125746	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.26	35	63.2	0.554	0.00000293	812
Missense in Polyphen		5	14.516	0.34445		204
Synonymous	-0.834	24	19.3	1.24	8.93e-7	213
Loss of Function	1.41	4	8.43	0.475	5.71e-7	87

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000742	0.000734
Ashkenazi Jewish	0.00	0.00
East Asian	0.000190	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000360	0.0000352
Middle Eastern	0.000190	0.000163
South Asian	0.000154	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the DNA-binding general RNA polymerase II transcription factor IID complex (TFIID). TFIID plays a critical role in the regulation of gene transcription in eukaryotic cells. {ECO:0000269|PubMed:9695952}.
• Disease: DISEASE: Mental retardation, autosomal recessive 60 (MRT60) [MIM:617432]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. In contrast to syndromic or specific mental retardation which also present with associated physical, neurological and/or psychiatric manifestations, intellectual deficiency is the only primary symptom of non-syndromic mental retardation. MRT60 patients display mild intellectual disability, delayed psychomotor development, learning difficulties, and poor overall growth with variable microcephaly. MRT60 inheritance is autosomal recessive. {ECO:0000269|PubMed:28257693}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Basal transcription factors - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);Eukaryotic Transcription Initiation;Disease;Gene expression (Transcription);Generic Transcription Pathway;Transcription of the HIV genome;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;RNA Polymerase II HIV Promoter Escape;RNA Polymerase II Pre-transcription Events;RNA Polymerase II Transcription Initiation;RNA Polymerase II Transcription Initiation And Promoter Clearance;HIV Transcription Initiation;RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription;Infectious disease;RNA Polymerase II Promoter Escape;RNA Polymerase II Transcription Pre-Initiation And Promoter Opening;Regulation of TP53 Activity through Phosphorylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53 (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.614
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.701
• hipred: Y
• hipred_score: 0.769
• ghis: 0.622

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.988

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Taf13

Gene ontology

• Biological process: DNA-templated transcription, initiation;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;snRNA transcription by RNA polymerase II;regulation of signal transduction by p53 class mediator
• Cellular component: nucleus;nucleoplasm;transcription factor TFIID complex;nucleolus
• Molecular function: DNA binding;DNA-binding transcription factor activity;transcription coregulator activity;protein binding;protein C-terminus binding;protein heterodimerization activity