rs1554110735
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1_StrongPP5_Very_Strong
The NM_001372066.1(TFAP2A):c.1043_1044del(p.Lys348ArgfsTer84) variant causes a frameshift change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Genomes: not found (cov: 32)
Consequence
TFAP2A
NM_001372066.1 frameshift
NM_001372066.1 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.02
Genes affected
TFAP2A (HGNC:11742): (transcription factor AP-2 alpha) The protein encoded by this gene is a transcription factor that binds the consensus sequence 5'-GCCNNNGGC-3'. The encoded protein functions as either a homodimer or as a heterodimer with similar family members. This protein activates the transcription of some genes while inhibiting the transcription of others. Defects in this gene are a cause of branchiooculofacial syndrome (BOFS). Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Dec 2009]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.21 CDS is truncated, and there are 2 pathogenic variants in the truncated region.
PP5
?
Variant 6-10398692-CTT-C is Pathogenic according to our data. Variant chr6-10398692-CTT-C is described in ClinVar as [Pathogenic]. Clinvar id is 523459.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TFAP2A | NM_001372066.1 | c.1043_1044del | p.Lys348ArgfsTer84 | frameshift_variant | 7/7 | ENST00000379613.10 | |
TFAP2A | NM_001032280.3 | c.1019_1020del | p.Lys340ArgfsTer84 | frameshift_variant | 7/7 | ||
TFAP2A | NM_001042425.3 | c.1025_1026del | p.Lys342ArgfsTer84 | frameshift_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TFAP2A | ENST00000379613.10 | c.1043_1044del | p.Lys348ArgfsTer84 | frameshift_variant | 7/7 | 1 | NM_001372066.1 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Branchiooculofacial syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Genetics Department, University Hospital of Toulouse | May 15, 2020 | This null variant affecting TFAP2A gene c.1037_1038del, p.(Lys346fs*84) is absent from GnomAD and was once reported in the Clinvar database as pathogenic (SCV000747548.1) - |
Amblyopia;C0014877:Esotropia;C0020534:Hypertelorism;C0023316:Lens subluxation;C0026010:Microphthalmia;C0028738:Nystagmus;C0151611:EEG abnormality;C0239234:Low-set ears;C0240063:Iris coloboma;C0240635:High palate;C0521525:Short neck;C0522214:Abnormality of visual evoked potentials;C0678230:Epicanthus Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Jan 01, 2017 | - - |
Computational scores
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at