rs771487311
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP3_ModeratePP5
The NM_001080463.2(DYNC2H1):c.10343T>C(p.Leu3448Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000852 in 1,549,064 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/20 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001080463.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DYNC2H1 | NM_001080463.2 | c.10343T>C | p.Leu3448Pro | missense_variant | 68/90 | ENST00000650373.2 | |
DYNC2H1 | NM_001377.3 | c.10322T>C | p.Leu3441Pro | missense_variant | 67/89 | ENST00000375735.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DYNC2H1 | ENST00000650373.2 | c.10343T>C | p.Leu3448Pro | missense_variant | 68/90 | NM_001080463.2 | A1 | ||
DYNC2H1 | ENST00000375735.7 | c.10322T>C | p.Leu3441Pro | missense_variant | 67/89 | 1 | NM_001377.3 | P3 | |
DYNC2H1 | ENST00000334267.11 | c.2205+121111T>C | intron_variant | 1 | |||||
ENST00000649070.1 | n.691-3226A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000192 AC: 3AN: 156656Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 82320
GnomAD4 exome AF: 0.0000881 AC: 123AN: 1396910Hom.: 0 Cov.: 30 AF XY: 0.0000784 AC XY: 54AN XY: 689030
GnomAD4 genome ? AF: 0.0000592 AC: 9AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74324
ClinVar
Submissions by phenotype
Asphyxiating thoracic dystrophy 3 Pathogenic:3Uncertain:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute | Jul 11, 2014 | This substitution is predicted to create a change of a leucine to a proline at amino acid position 3448, NP_001073932.1(DYNC2H1): p.Leu3448). The leucine at this position is highly conserved and is located in the ATP-binding dynein motor region D5.Grantham assessment is likely deleterious due to conservation and amino acid properties. In-silico software predicts this variant to be disease-causing. This is a novel variant not present in disease or population databases. It was identified in a patient with clinical and radiographic features of JATD, and a second novel missense variant in teh DYNC2H1 gene was present in trans. - |
Uncertain significance, no assertion criteria provided | research | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
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 | - - |
Jeune thoracic dystrophy Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Nov 14, 2023 | This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 3448 of the DYNC2H1 protein (p.Leu3448Pro). This variant is present in population databases (rs771487311, gnomAD 0.005%). This missense change has been observed in individual(s) with DYNC2H1-related conditions (PMID: 24183451, 26938784, 29068549). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 369661). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt DYNC2H1 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic. - |
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 | - - |
Short-rib thoracic dysplasia 6 with or without polydactyly 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 | - - |
not provided Pathogenic:1Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center | Feb 17, 2021 | PM2 - |
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Jul 17, 2023 | Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 34040173, 26938784, 28832562, 24183451, 29068549, 29453417, 27535533, 36442996, Buchh2023[Abstract]) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at