rs1555804780
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_001257096.2(PAX1):c.1169_1173dup(p.Pro392AlafsTer19) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
PAX1
NM_001257096.2 frameshift
NM_001257096.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.34
Genes affected
PAX1 (HGNC:8615): (paired box 1) This gene is a member of the paired box (PAX) family of transcription factors. Members of the PAX family typically contain a paired box domain and a paired-type homeodomain. These genes play critical roles during fetal development. This gene plays a role in pattern formation during embryogenesis and may be essential for development of the vertebral column. This gene is silenced by methylation in ovarian and cervical cancers and may be a tumor suppressor gene. Mutations in this gene are also associated with vertebral malformations. [provided by RefSeq, Mar 2012]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 20-21709329-G-GGGCCC is Pathogenic according to our data. Variant chr20-21709329-G-GGGCCC is described in ClinVar as [Likely_pathogenic]. Clinvar id is 522604.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAX1 | NM_001257096.2 | c.1169_1173dup | p.Pro392AlafsTer19 | frameshift_variant | 4/5 | ENST00000613128.5 | |
PAX1 | NM_006192.5 | c.1169_1173dup | p.Pro392AlafsTer19 | frameshift_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAX1 | ENST00000613128.5 | c.1169_1173dup | p.Pro392AlafsTer19 | frameshift_variant | 4/5 | 1 | NM_001257096.2 | P1 | |
PAX1 | ENST00000398485.6 | c.1169_1173dup | p.Pro392AlafsTer19 | frameshift_variant | 4/5 | 5 | |||
PAX1 | ENST00000444366.2 | c.1097_1101dup | p.Pro368AlafsTer19 | frameshift_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 33
GnomAD4 exome
Cov.:
33
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Otofaciocervical syndrome 2 Pathogenic:2
Likely pathogenic, criteria provided, single submitter | research | Diagnostics Division, CENTRE FOR DNA FINGERPRINTING AND DIAGNOSTICS | Jan 01, 2017 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 26, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at