19-3730627-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001267560.2(TJP3):c.534C>T(p.Ser178Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000354 in 1,611,852 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0017 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00022 ( 2 hom. )
Consequence
TJP3
NM_001267560.2 synonymous
NM_001267560.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -6.20
Genes affected
TJP3 (HGNC:11829): (tight junction protein 3) The protein encoded by this gene is a member of the membrane-associated guanylate kinase-like (MAGUK) protein family which is characterized by members having multiple PDZ domains, a single SH3 domain, and a single guanylate kinase-like (GUK)-domain. In addition, members of the zonula occludens protein subfamily have an acidic domain, a basic arginine-rich region, and a proline-rich domain. The protein encoded by this gene plays a role in the linkage between the actin cytoskeleton and tight-junctions and also sequesters cyclin D1 at tight junctions during mitosis. Alternative splicing results in multiple transcript variants encoding distinct isoforms. This gene has a partial pseudogene on chromosome 1. [provided by RefSeq, May 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
Variant 19-3730627-C-T is Benign according to our data. Variant chr19-3730627-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2649007.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-6.2 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TJP3 | NM_001267560.2 | c.534C>T | p.Ser178Ser | synonymous_variant | 5/21 | ENST00000541714.7 | NP_001254489.1 | |
TJP3 | NM_001267561.2 | c.561C>T | p.Ser187Ser | synonymous_variant | 5/21 | NP_001254490.1 | ||
TJP3 | XM_047438611.1 | c.732C>T | p.Ser244Ser | synonymous_variant | 5/21 | XP_047294567.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TJP3 | ENST00000541714.7 | c.534C>T | p.Ser178Ser | synonymous_variant | 5/21 | 2 | NM_001267560.2 | ENSP00000439278.1 | ||
TJP3 | ENST00000587686.1 | c.591C>T | p.Ser197Ser | synonymous_variant | 4/20 | 1 | ENSP00000467864.1 | |||
TJP3 | ENST00000589378.5 | c.561C>T | p.Ser187Ser | synonymous_variant | 5/21 | 2 | ENSP00000465419.1 | |||
TJP3 | ENST00000539908.6 | c.426C>T | p.Ser142Ser | synonymous_variant | 4/20 | 2 | ENSP00000439991.1 |
Frequencies
GnomAD3 genomes AF: 0.00166 AC: 252AN: 152194Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.000467 AC: 114AN: 243860Hom.: 2 AF XY: 0.000330 AC XY: 44AN XY: 133238
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GnomAD4 exome AF: 0.000215 AC: 314AN: 1459540Hom.: 2 Cov.: 32 AF XY: 0.000180 AC XY: 131AN XY: 726216
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GnomAD4 genome AF: 0.00168 AC: 256AN: 152312Hom.: 2 Cov.: 32 AF XY: 0.00156 AC XY: 116AN XY: 74488
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2022 | TJP3: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at