5-13777309-G-A
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_001369.3(DNAH5):c.8998C>T(p.Arg3000*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,613,202 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 Likely pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001369.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAH5 | ENST00000265104.5 | c.8998C>T | p.Arg3000* | stop_gained | 54/79 | 1 | NM_001369.3 | ENSP00000265104.4 | ||
DNAH5 | ENST00000681290.1 | c.8953C>T | p.Arg2985* | stop_gained | 54/79 | ENSP00000505288.1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152074Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250708Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135474
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461128Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 726860
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74286
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Pathogenic:2
Pathogenic, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 23, 2024 | This sequence change creates a premature translational stop signal (p.Arg3000*) in the DNAH5 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DNAH5 are known to be pathogenic (PMID: 11788826, 16627867). This variant is present in population databases (rs769054713, gnomAD 0.006%). This premature translational stop signal has been observed in individual(s) with clinical features of primary ciliary dyskinesia and/or primary ciliary dyskinesia (PMID: 22416021; internal data). 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: 188388). For these reasons, this variant has been classified as Pathogenic. - |
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Oct 10, 2022 | Observed with another DNAH5 variant in a patient with PCD in published literature, but it is not known whether the variants occurred on the same (in cis) or on different (in trans) chromosomes (Djakow et al., 2012); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 22416021) - |
DNAH5-related disorder Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 05, 2024 | The DNAH5 c.8998C>T variant is predicted to result in premature protein termination (p.Arg3000*). This variant was reported in an individual with primary ciliary dyskinesia (Djakow et al. 2012. PubMed ID: 22416021). This variant is reported in 0.0054% of alleles in individuals of East Asian descent in gnomAD and is interpreted as pathogenic/likely pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/188388/). Loss-of-function variants in DNAH5 are expected to be pathogenic (Olbrich et al. 2002. PubMed ID: 11788826; Hornef et al. 2006. PubMed ID: 16627867). This variant is interpreted as pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at