rs1555082470
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001377.3(DYNC2H1):c.10603C>T(p.Gln3535*) variant causes a stop gained, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001377.3 stop_gained, splice_region
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 |
---|---|---|---|---|---|---|---|---|
DYNC2H1 | NM_001080463.2 | c.10624C>T | p.Gln3542* | stop_gained, splice_region_variant | 70/90 | ENST00000650373.2 | NP_001073932.1 | |
DYNC2H1 | NM_001377.3 | c.10603C>T | p.Gln3535* | stop_gained, splice_region_variant | 69/89 | ENST00000375735.7 | NP_001368.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DYNC2H1 | ENST00000650373.2 | c.10624C>T | p.Gln3542* | stop_gained, splice_region_variant | 70/90 | NM_001080463.2 | ENSP00000497174.1 | |||
DYNC2H1 | ENST00000375735.7 | c.10603C>T | p.Gln3535* | stop_gained, splice_region_variant | 69/89 | 1 | NM_001377.3 | ENSP00000364887.2 | ||
DYNC2H1 | ENST00000334267.11 | c.2205+123330C>T | intron_variant | 1 | ENSP00000334021.7 | |||||
ENSG00000285878 | ENST00000649070.1 | n.691-5445G>A | intron_variant |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 6.97e-7 AC: 1AN: 1434056Hom.: 0 Cov.: 30 AF XY: 0.00000141 AC XY: 1AN XY: 710936
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Asphyxiating thoracic dystrophy 3 Pathogenic:2
Likely pathogenic, no assertion criteria provided | research | University of Washington Center for Mendelian Genomics, University of Washington | - | - - |
Pathogenic, no assertion criteria provided | research | Dan Cohn Lab, University Of California Los Angeles | Jun 01, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at