GeneBe

rs41486346

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000437147.8(TAF1):​n.1359-9849_1359-9839delTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., 0 hem., cov: 19)

Consequence

TAF1
ENST00000437147.8 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.66

Publications

0 publications found
Variant links:
Genes affected
TAF1 (HGNC:11535): (TATA-box binding protein associated factor 1) Initiation of transcription by RNA polymerase II requires the activities of more than 70 polypeptides. The protein that coordinates these activities is the basal transcription factor 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 the largest subunit of TFIID. This subunit binds to core promoter sequences encompassing the transcription start site. It also binds to activators and other transcriptional regulators, and these interactions affect the rate of transcription initiation. This subunit contains two independent protein kinase domains at the N- and C-terminals, but also possesses acetyltransferase activity and can act as a ubiquitin-activating/conjugating enzyme. Mutations in this gene result in Dystonia 3, torsion, X-linked, a dystonia-parkinsonism disorder. Alternative splicing of this gene results in multiple transcript variants. This gene is part of a complex transcription unit (TAF1/DYT3), wherein some transcript variants share exons with TAF1 as well as additional downstream DYT3 exons. [provided by RefSeq, Oct 2013]
TAF1 Gene-Disease associations (from GenCC):
  • intellectual disability, X-linked, syndromic 33
    Inheritance: XL Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P, Illumina
  • X-linked dystonia-parkinsonism
    Inheritance: XL, Unknown Classification: STRONG, MODERATE, SUPPORTIVE, LIMITED Submitted by: Ambry Genetics, Genomics England PanelApp, Orphanet, Labcorp Genetics (formerly Invitae)
  • X-linked intellectual disability-global development delay-facial dysmorphism-sacral caudal remnant syndrome
    Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TAF1NR_104387.2 linkn.5520-9839_5520-9829delTTTTTTTTTTT intron_variant Intron 38 of 39
TAF1NR_104388.2 linkn.5511-9839_5511-9829delTTTTTTTTTTT intron_variant Intron 38 of 39
TAF1NR_104389.2 linkn.5418-9839_5418-9829delTTTTTTTTTTT intron_variant Intron 37 of 38

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TAF1ENST00000437147.8 linkn.1359-9849_1359-9839delTTTTTTTTTTT intron_variant Intron 12 of 13 1 ENSP00000406517.4
TAF1ENST00000462588.5 linkn.999-9849_999-9839delTTTTTTTTTTT intron_variant Intron 9 of 10 1 ENSP00000508350.1
TAF1ENST00000467309.5 linkn.*107-9849_*107-9839delTTTTTTTTTTT intron_variant Intron 3 of 5 1 ENSP00000507353.1

Frequencies

GnomAD3 genomes
AF:
0.0000126
AC:
1
AN:
79199
Hom.:
0
Cov.:
19
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000246
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0000126
AC:
1
AN:
79199
Hom.:
0
Cov.:
19
AF XY:
0.00
AC XY:
0
AN XY:
18561
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
21039
American (AMR)
AF:
0.00
AC:
0
AN:
7093
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2065
East Asian (EAS)
AF:
0.00
AC:
0
AN:
2427
South Asian (SAS)
AF:
0.00
AC:
0
AN:
1590
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
2574
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
168
European-Non Finnish (NFE)
AF:
0.0000246
AC:
1
AN:
40686
Other (OTH)
AF:
0.00
AC:
0
AN:
1029
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.375
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
0.00
Hom.:
8
Bravo
AF:
0.0000189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs41486346; hg19: chrX-70738542; API