12-110628808-G-T
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_001082538.3(TCTN1):c.514G>T(p.Glu172*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000343 in 1,459,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001082538.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TCTN1 | ENST00000397659.9 | c.514G>T | p.Glu172* | stop_gained | 4/15 | 1 | NM_001082538.3 | ENSP00000380779.4 | ||
TCTN1 | ENST00000551590.5 | c.514G>T | p.Glu172* | stop_gained | 4/15 | 1 | ENSP00000448735.1 | |||
TCTN1 | ENST00000397655.7 | c.514G>T | p.Glu172* | stop_gained | 4/15 | 1 | ENSP00000380775.3 | |||
TCTN1 | ENST00000397656.8 | n.*147G>T | non_coding_transcript_exon_variant | 5/16 | 2 | ENSP00000380776.4 | ||||
TCTN1 | ENST00000480648.5 | n.514G>T | non_coding_transcript_exon_variant | 4/16 | 5 | ENSP00000437196.1 | ||||
TCTN1 | ENST00000495659.6 | n.*272G>T | non_coding_transcript_exon_variant | 4/15 | 2 | ENSP00000436673.2 | ||||
TCTN1 | ENST00000397656.8 | n.*147G>T | 3_prime_UTR_variant | 5/16 | 2 | ENSP00000380776.4 | ||||
TCTN1 | ENST00000495659.6 | n.*272G>T | 3_prime_UTR_variant | 4/15 | 2 | ENSP00000436673.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1459832Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 726386
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Meckel-Gruber syndrome;C0431399:Familial aplasia of the vermis Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 30, 2024 | This sequence change creates a premature translational stop signal (p.Glu172*) in the TCTN1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TCTN1 are known to be pathogenic (PMID: 21725307, 22693042, 27894351). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TCTN1-related conditions. For these reasons, this variant has been classified as Pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.