rs1554403626
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_012338.4(TSPAN12):c.218_219insGCTGTTT(p.Phe73LeufsTer46) 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 Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
TSPAN12
NM_012338.4 frameshift
NM_012338.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.94
Genes affected
TSPAN12 (HGNC:21641): (tetraspanin 12) The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. [provided by RefSeq, Jul 2008]
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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 7-120838843-G-GAAACAGC is Pathogenic according to our data. Variant chr7-120838843-G-GAAACAGC is described in ClinVar as [Pathogenic]. Clinvar id is 321.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSPAN12 | NM_012338.4 | c.218_219insGCTGTTT | p.Phe73LeufsTer46 | frameshift_variant | 4/8 | ENST00000222747.8 | |
TSPAN12 | XM_005250239.4 | c.218_219insGCTGTTT | p.Phe73LeufsTer46 | frameshift_variant | 5/9 | ||
TSPAN12 | XM_047420095.1 | c.218_219insGCTGTTT | p.Phe73LeufsTer46 | frameshift_variant | 5/9 | ||
TSPAN12 | XM_047420096.1 | c.218_219insGCTGTTT | p.Phe73LeufsTer47 | frameshift_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSPAN12 | ENST00000222747.8 | c.218_219insGCTGTTT | p.Phe73LeufsTer46 | frameshift_variant | 4/8 | 1 | NM_012338.4 | P1 |
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: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Exudative vitreoretinopathy 5 Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 12, 2010 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Genetics and Molecular Pathology, SA Pathology | Oct 11, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at