rs397514635
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PM5PP5_Moderate
The NM_001080463.2(DYNC2H1):c.7985G>A(p.Arg2662Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,612,452 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2662W) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001080463.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DYNC2H1 | NM_001080463.2 | c.7985G>A | p.Arg2662Gln | missense_variant | 49/90 | ENST00000650373.2 | |
DYNC2H1 | NM_001377.3 | c.7985G>A | p.Arg2662Gln | missense_variant | 49/89 | ENST00000375735.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DYNC2H1 | ENST00000650373.2 | c.7985G>A | p.Arg2662Gln | missense_variant | 49/90 | NM_001080463.2 | A1 | ||
DYNC2H1 | ENST00000375735.7 | c.7985G>A | p.Arg2662Gln | missense_variant | 49/89 | 1 | NM_001377.3 | P3 | |
DYNC2H1 | ENST00000334267.11 | c.2205+64954G>A | intron_variant | 1 | |||||
DYNC2H1 | ENST00000649323.1 | c.*5509G>A | 3_prime_UTR_variant, NMD_transcript_variant | 47/51 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152008Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248420Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134768
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1460444Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 726518
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152008Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74234
ClinVar
Submissions by phenotype
Asphyxiating thoracic dystrophy 3 Pathogenic:4
Likely pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | - | The c.7985G>A (p.R2662Q) variant in the DYNC2H1 gene has been identified in a compound heterozygous state in multiple individuals with short-rib thoracic dysplasia (PMID: 22499340, 29068549). - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 2012 | - - |
Pathogenic, no assertion criteria provided | research | Dan Cohn Lab, University Of California Los Angeles | Jun 01, 2017 | - - |
Likely pathogenic, no assertion criteria provided | research | University of Washington Center for Mendelian Genomics, University of Washington | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at