chr8-119803881-G-C
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_003184.4(TAF2):c.557C>G(p.Thr186Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Consequence
TAF2
NM_003184.4 missense
NM_003184.4 missense
Scores
5
9
5
Clinical Significance
Conservation
PhyloP100: 9.95
Publications
2 publications found
Genes affected
TAF2 (HGNC:11536): (TATA-box binding protein associated factor 2) 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 one of the larger subunits of TFIID that is stably associated with the TFIID complex. It contributes to interactions at and downstream of the transcription initiation site, interactions that help determine transcription complex response to activators. [provided by RefSeq, Jul 2008]
TAF2 Gene-Disease associations (from GenCC):
- microcephaly-thin corpus callosum-intellectual disability syndromeInheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE, LIMITED Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.848
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TAF2 | ENST00000378164.7 | c.557C>G | p.Thr186Arg | missense_variant | Exon 5 of 26 | 1 | NM_003184.4 | ENSP00000367406.2 | ||
TAF2 | ENST00000686879.1 | c.557C>G | p.Thr186Arg | missense_variant | Exon 5 of 27 | ENSP00000509206.1 | ||||
TAF2 | ENST00000685235.1 | c.557C>G | p.Thr186Arg | missense_variant | Exon 5 of 26 | ENSP00000510174.1 | ||||
TAF2 | ENST00000688645.1 | c.557C>G | p.Thr186Arg | missense_variant | Exon 5 of 25 | ENSP00000509978.1 | ||||
TAF2 | ENST00000523904.2 | c.557C>G | p.Thr186Arg | missense_variant | Exon 5 of 25 | 3 | ENSP00000430832.2 | |||
TAF2 | ENST00000690144.1 | c.557C>G | p.Thr186Arg | missense_variant | Exon 5 of 26 | ENSP00000510548.1 | ||||
TAF2 | ENST00000521007.2 | c.557C>G | p.Thr186Arg | missense_variant | Exon 6 of 7 | 3 | ENSP00000428484.2 | |||
TAF2 | ENST00000685202.1 | n.557C>G | non_coding_transcript_exon_variant | Exon 5 of 27 | ENSP00000509214.1 | |||||
TAF2 | ENST00000685503.1 | n.557C>G | non_coding_transcript_exon_variant | Exon 5 of 26 | ENSP00000509198.1 | |||||
TAF2 | ENST00000685663.1 | n.*429C>G | non_coding_transcript_exon_variant | Exon 7 of 28 | ENSP00000508988.1 | |||||
TAF2 | ENST00000685824.1 | n.*372C>G | non_coding_transcript_exon_variant | Exon 4 of 24 | ENSP00000510262.1 | |||||
TAF2 | ENST00000685876.1 | n.*275C>G | non_coding_transcript_exon_variant | Exon 6 of 27 | ENSP00000510493.1 | |||||
TAF2 | ENST00000685993.1 | n.*372C>G | non_coding_transcript_exon_variant | Exon 4 of 25 | ENSP00000510102.1 | |||||
TAF2 | ENST00000686098.1 | n.557C>G | non_coding_transcript_exon_variant | Exon 5 of 25 | ENSP00000509102.1 | |||||
TAF2 | ENST00000689164.1 | n.557C>G | non_coding_transcript_exon_variant | Exon 5 of 24 | ENSP00000508729.1 | |||||
TAF2 | ENST00000689919.1 | n.*275C>G | non_coding_transcript_exon_variant | Exon 6 of 26 | ENSP00000510768.1 | |||||
TAF2 | ENST00000690808.1 | n.557C>G | non_coding_transcript_exon_variant | Exon 5 of 26 | ENSP00000509791.1 | |||||
TAF2 | ENST00000690922.1 | n.557C>G | non_coding_transcript_exon_variant | Exon 5 of 26 | ENSP00000509498.1 | |||||
TAF2 | ENST00000691880.1 | n.*213C>G | non_coding_transcript_exon_variant | Exon 4 of 25 | ENSP00000508515.1 | |||||
TAF2 | ENST00000692518.1 | n.*372C>G | non_coding_transcript_exon_variant | Exon 4 of 25 | ENSP00000508959.1 | |||||
TAF2 | ENST00000692707.1 | n.*275C>G | non_coding_transcript_exon_variant | Exon 6 of 28 | ENSP00000509024.1 | |||||
TAF2 | ENST00000685663.1 | n.*429C>G | 3_prime_UTR_variant | Exon 7 of 28 | ENSP00000508988.1 | |||||
TAF2 | ENST00000685824.1 | n.*372C>G | 3_prime_UTR_variant | Exon 4 of 24 | ENSP00000510262.1 | |||||
TAF2 | ENST00000685876.1 | n.*275C>G | 3_prime_UTR_variant | Exon 6 of 27 | ENSP00000510493.1 | |||||
TAF2 | ENST00000685993.1 | n.*372C>G | 3_prime_UTR_variant | Exon 4 of 25 | ENSP00000510102.1 | |||||
TAF2 | ENST00000689919.1 | n.*275C>G | 3_prime_UTR_variant | Exon 6 of 26 | ENSP00000510768.1 | |||||
TAF2 | ENST00000691880.1 | n.*213C>G | 3_prime_UTR_variant | Exon 4 of 25 | ENSP00000508515.1 | |||||
TAF2 | ENST00000692518.1 | n.*372C>G | 3_prime_UTR_variant | Exon 4 of 25 | ENSP00000508959.1 | |||||
TAF2 | ENST00000692707.1 | n.*275C>G | 3_prime_UTR_variant | Exon 6 of 28 | ENSP00000509024.1 | |||||
TAF2 | ENST00000685684.1 | n.520+37C>G | intron_variant | Intron 5 of 24 | ENSP00000509441.1 | |||||
TAF2 | ENST00000688037.1 | n.139-1856C>G | intron_variant | Intron 2 of 22 | ENSP00000510169.1 | |||||
TAF2 | ENST00000690031.1 | n.*238+37C>G | intron_variant | Intron 6 of 9 | ENSP00000508549.1 | |||||
TAF2 | ENST00000691847.1 | n.538+19C>G | intron_variant | Intron 5 of 23 | ENSP00000509663.1 | |||||
TAF2 | ENST00000692916.1 | n.419-1856C>G | intron_variant | Intron 4 of 24 | ENSP00000509603.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Mar 01, 2019
CeGaT Center for Human Genetics Tuebingen
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Microcephaly-thin corpus callosum-intellectual disability syndrome Uncertain:1
Dec 01, 2013
OMIM
Significance:Uncertain significance
Review Status:no assertion criteria provided
Collection Method:literature only
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Pathogenic
D
MetaSVM
Benign
T
MutationAssessor
Benign
L
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
P
Vest4
MutPred
Gain of MoRF binding (P = 0.1401);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: 37
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.