rs267607228
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001042545.2(LTBP4):c.2481C>A(p.Cys827Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000069 in 1,449,584 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001042545.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LTBP4 | NM_001042545.2 | c.2481C>A | p.Cys827Ter | stop_gained | 17/30 | ENST00000396819.8 | NP_001036010.1 | |
LTBP4 | NM_001042544.1 | c.2682C>A | p.Cys894Ter | stop_gained | 20/33 | NP_001036009.1 | ||
LTBP4 | NM_003573.2 | c.2571C>A | p.Cys857Ter | stop_gained | 20/33 | NP_003564.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LTBP4 | ENST00000396819.8 | c.2481C>A | p.Cys827Ter | stop_gained | 17/30 | 1 | NM_001042545.2 | ENSP00000380031 | P3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000440 AC: 1AN: 227046Hom.: 0 AF XY: 0.00000812 AC XY: 1AN XY: 123206
GnomAD4 exome AF: 6.90e-7 AC: 1AN: 1449584Hom.: 0 Cov.: 34 AF XY: 0.00000139 AC XY: 1AN XY: 720024
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Cutis laxa with severe pulmonary, gastrointestinal and urinary anomalies Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 01, 2009 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at