chr11-65557827-GC-G
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1PP5_Very_Strong
The NM_001130144.3(LTBP3):βc.132delGβ(p.Pro45ArgfsTer25) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 1,462,020 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (β β ). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001130144.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LTBP3 | NM_001130144.3 | c.132delG | p.Pro45ArgfsTer25 | frameshift_variant | Exon 1 of 28 | ENST00000301873.11 | NP_001123616.1 | |
LTBP3 | NM_021070.4 | c.132delG | p.Pro45ArgfsTer25 | frameshift_variant | Exon 1 of 27 | NP_066548.2 | ||
LTBP3 | NM_001164266.1 | c.-216delG | 5_prime_UTR_variant | Exon 1 of 27 | NP_001157738.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 150968Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000458 AC: 6AN: 1311052Hom.: 0 Cov.: 31 AF XY: 0.00000619 AC XY: 4AN XY: 646290
GnomAD4 genome AF: 0.0000132 AC: 2AN: 150968Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 73704
ClinVar
Submissions by phenotype
Brachyolmia-amelogenesis imperfecta syndrome Pathogenic:3
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Frameshift: predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant (PVS1_VS). The variant has been reported to be associated with LTBP3 related disorder (ClinVar ID: VCV000523637, PMID:29625025). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000047, PM2_M). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -
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not provided Pathogenic:1
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Heritable Thoracic Aortic Disease Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at