rs201144827
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004817.4(TJP2):c.3557G>A(p.Arg1186Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00007 in 1,614,056 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1186G) has been classified as Uncertain significance.
Frequency
Consequence
NM_004817.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TJP2 | NM_004817.4 | c.3557G>A | p.Arg1186Gln | missense_variant | 23/23 | ENST00000377245.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TJP2 | ENST00000377245.9 | c.3557G>A | p.Arg1186Gln | missense_variant | 23/23 | 1 | NM_004817.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251308Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135822
GnomAD4 exome AF: 0.0000739 AC: 108AN: 1461874Hom.: 0 Cov.: 30 AF XY: 0.0000646 AC XY: 47AN XY: 727238
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 10, 2014 | The p.Arg1016Gln variant in TJP2 has not been previously reported in individuals with hearing loss, but has been identified in 2/8600 of European American chrom osomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS/; dbSNP rs201144827). Although this variant has been seen in the general populat ion, its frequency is not high enough to rule out a pathogenic role. Computation al prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. In summary, the clinical significance of th e p.Arg1016Gln variant is uncertain. - |
Cholestasis, progressive familial intrahepatic, 4;C5542604:Hypercholanemia, familial 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 13, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at