TAF1L

protein-coding

TATA-box binding protein associated factor 1 like, the group of Bromodomain containing

Gene summary

This locus is intronless, and apparently arose in the primate lineage from retrotransposition of the transcript from the multi-exon TAF1 locus on the X chromosome. The gene is expressed in male germ cells, and the product has been shown to function interchangeably with the TAF1 product. [provided by RefSeq, Aug 2015]

MANE transcript

NM_153809.2

Inheritance

—

ClinVar variants

U:232B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr9:32,629,454-32,635,669

External References & Databases

Ensembl (ENSG00000122728)

Transcript & Mutation Effects

hg38 • Region Span ~6.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TAF1L variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 236

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153809.2. 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			229 clinvar	8 clinvar	1 clinvar	238
nonsense			1 clinvar			1
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)						0
Total	0	0	232	11	1	244

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153809.2	RefSeq	NP_722516.1	1	MANE Select
ENST00000242310.4	Ensembl	ENSP00000418379.1	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Basal transcription factors - Homo sapiens (human)
Disease
Gene expression (Transcription)
Generic Transcription Pathway
Transcription of the HIV genome

Biological Process

regulation of transcription by RNA polymerase II
transcription by RNA polymerase II
transcription initiation from RNA polymerase II promoter
protein phosphorylation
male meiotic nuclear division

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
histone acetyltransferase activity
protein serine/threonine kinase activity
TBP-class protein binding
sequence-specific DNA binding

Cellular Component

cellular_component
nucleoplasm
transcription factor TFIID complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000242310
Coding exons: 1
Length: 6216
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.403	993	958	1.04	0.0000570	12102
Missense (PolyPhen)		283	308.72	0.91668		3956
Synonymous	-1.14	373	346	1.08	0.0000182	3525
Loss of Function	5.36	9	49.9	0.180	0.00000309	680

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as a functional substitute for TAF1/TAFII250 during male meiosis, when sex chromosomes are transcriptionally silenced. {ECO:0000269|PubMed:12217962}.;

Intolerance Scores

LoFtool: 0.582
RVIS EVS: -0.6
RVIS percentile EVS: 17.75

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.544

Gene Damage Prediction

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