TAF13

protein-coding

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

Gene summary

Initiation of transcription by RNA polymerase II requires the activities of more than 70 polypeptides. The protein that coordinates these activities is transcription factor IID (TFIID), which binds to the core promoter to position the polymerase properly, serves as the scaffold for assembly of the remainder of the transcription complex, and acts as a channel for regulatory signals. TFIID is composed of the TATA-binding protein (TBP) and a group of evolutionarily conserved proteins known as TBP-associated factors or TAFs. TAFs may participate in basal transcription, serve as coactivators, function in promoter recognition or modify general transcription factors (GTFs) to facilitate complex assembly and transcription initiation. This gene encodes a small subunit associated with a subset of TFIID complexes. This subunit interacts with TBP and with two other small subunits of TFIID, TAF10 and TAF11. There is a pseudogene located on chromosome 6. [provided by RefSeq, Jul 2008]

Previous symbols:

TAF2K

MANE transcript

NM_005645.4

Inheritance

ClinVar variants

P:3U:7B:3

Top phenotype

Intellectual developmental disorder, autosomal recessive 60

gnomAD constraint

pLI —, LoF o/e 0.47

Max pathogenic AF

—

Genomic locus

chr1:109,062,496-109,076,012

External References & Databases

Ensembl (ENSG00000197780)

Transcript & Mutation Effects

hg38 • Region Span ~13.5 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

intellectual developmental disorder, autosomal recessive 60STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0044313

Submitter: G2P

autosomal recessive primary microcephalySUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0016660

Submitter: Orphanet

intellectual developmental disorder, autosomal recessive 60MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0044313

Submitter: PanelApp Australia

intellectual developmental disorder, autosomal recessive 60LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0044313

Submitter: Labcorp Genetics (formerly Invitae)

intellectual developmental disorder, autosomal recessive 60LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0044313

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Intellectual developmental disorder, autosomal recessive 60AR

Manifestation: Endocrine; Neurologic

Intervention: General

Rationale: 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

Refs: 28257693

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TAF13 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 5

Intellectual disability, autosomal recessive 60Total: 4

not providedTotal: 3

TAF13-related disorderTotal: 2

Autosomal recessive primary microcephalyTotal: 1

Inborn genetic diseasesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005645.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar		3
missense	1 clinvar	1 clinvar	6 clinvar			8
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)		1 clinvar				1
Total	1	2	7	3	0	13

Highest pathogenic variant AF is 0.0000020744249

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005645.4	RefSeq	NP_005636.1	4	MANE Select
ENST00000338366.6	Ensembl	ENSP00000355051.4	4	MANE Select
ENST00000461096.7	Ensembl	ENSP00000433883.2	2	Standard
ENST00000692048.1	Ensembl	ENSP00000508876.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Basal transcription factors - Homo sapiens (human)
Herpes simplex infection - Homo sapiens (human)
Eukaryotic Transcription Initiation
Disease
Gene expression (Transcription)

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

Molecular Function

DNA binding
DNA-binding transcription factor activity
transcription coregulator activity
protein binding
protein C-terminus binding

Cellular Component

nucleus
nucleoplasm
transcription factor TFIID complex
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000338366
Coding exons: 4
Length: 13517
Individuals with no LoFs: 125721
Homozygous LoFs: 0
Heterozygous LoFs: 25
Defined: 125746
p: 0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.26	35	63.2	0.554	0.00000293	812
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00056	0.00055	rare
Latino/Admixed American	0.00018	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00019	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0.00015	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.149

Intolerance Scores

LoFtool: 0.614
RVIS EVS: -0.05
RVIS percentile EVS: 49.39

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.988

Gene Damage Prediction

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