NM_024809.5:c.254_255delTG
Variant summary
Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_024809.5(TCTN2):c.254_255delTG(p.Val85AspfsTer24) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. V85V) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_024809.5 frameshift
Scores
Clinical Significance
Conservation
Publications
- Joubert syndrome 24Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: ClinGen, G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
- Joubert syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- Meckel syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Pathogenic. The variant received 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TCTN2 | NM_024809.5 | c.254_255delTG | p.Val85AspfsTer24 | frameshift_variant | Exon 3 of 18 | ENST00000303372.7 | NP_079085.2 | |
TCTN2 | NM_001143850.3 | c.254_255delTG | p.Val85AspfsTer23 | frameshift_variant | Exon 3 of 18 | NP_001137322.1 | ||
TCTN2 | NM_001410989.1 | c.254_255delTG | p.Val85AspfsTer24 | frameshift_variant | Exon 3 of 17 | NP_001397918.1 | ||
TCTN2 | XM_017019974.2 | c.254_255delTG | p.Val85AspfsTer23 | frameshift_variant | Exon 3 of 17 | XP_016875463.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at