chr5-13864632-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP3_ModeratePP5
The NM_001369.3(DNAH5):c.4361G>A(p.Arg1454Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000141 in 1,614,038 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001369.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAH5 | ENST00000265104.5 | c.4361G>A | p.Arg1454Gln | missense_variant | Exon 28 of 79 | 1 | NM_001369.3 | ENSP00000265104.4 | ||
DNAH5 | ENST00000681290.1 | c.4316G>A | p.Arg1439Gln | missense_variant | Exon 28 of 79 | ENSP00000505288.1 | ||||
ENSG00000251423 | ENST00000503244.2 | n.253+4077C>T | intron_variant | Intron 1 of 2 | 4 | |||||
ENSG00000251423 | ENST00000637153.1 | n.213+4117C>T | intron_variant | Intron 1 of 2 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152082Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000836 AC: 21AN: 251286Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135800
GnomAD4 exome AF: 0.000142 AC: 207AN: 1461838Hom.: 0 Cov.: 33 AF XY: 0.000136 AC XY: 99AN XY: 727226
GnomAD4 genome AF: 0.000138 AC: 21AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74406
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Pathogenic:2Uncertain:2
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The p.R1454Q variant (also known as c.4361G>A), located in coding exon 28 of the DNAH5 gene, results from a G to A substitution at nucleotide position 4361. The arginine at codon 1454 is replaced by glutamine, an amino acid with highly similar properties. This variant was detected in two siblings with primary ciliary dyskensia (characterized by outer dynein arm defects on electron microscopy) who were compound heterozygous for another DNAH5 mutation; both siblings had immotile cilia and one sibling had situs inversus (Olbrich H, Nat. Genet. 2002 Feb; 30(2):143-4; Olbrich H, Pediatr. Res. 2006 Mar; 59(3):418-22). Ex vivo cultures of these patients' epithelial airway showed absent cilia or membrane alterations in many cells and mislocalization of DNAH5 to the basal body region in the remaining cells (Olbrich H, Pediatr. Res. 2006 Mar; 59(3):418-22). Based on the available evidence, p.R1454Q is classified as a pathogenic mutation. -
This sequence change in DNAH5 is predicted to replace arginine with glutamine at codon 1454, p.(Arg1454Gln). The arginine residue is moderately conserved (100 vertebrates, Multiz Alignments), and is located in the coiled-coiled stem region. There is a small physicochemical difference between arginine and glutamine. The highest population minor allele frequency in the population database gnomAD v4.0 is 0.02% (199/1,179,988 alleles) in the European (non-Finnish) population, which is consistent with recessive disease. This variant has been observed in trans with a pathogenic variant in two siblings with primary ciliary dyskinesia in a single family (PMID: 11788826, 25186273). It has conflicting interpretations in ClinVar (ID: 287698). Computational evidence is uninformative for the missense substitution (REVEL = 0.510). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.6.1, this variant is classified as a VARIANT OF UNCERTAIN SIGNIFICANCE. Following criteria are met: PM3, PM2_Supporting, PP1. -
This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 1454 of the DNAH5 protein (p.Arg1454Gln). This variant is present in population databases (rs542708170, gnomAD 0.02%). This missense change has been observed in individual(s) with primary ciliary dyskinesia (PMID: 11788826). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 287698). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt DNAH5 protein function with a negative predictive value of 95%. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -
Primary ciliary dyskinesia 3 Pathogenic:2Uncertain:1
The DNAH5 c.4361G>A (p.Arg1454Gln) variant is a missense variant that has has been reported in four studies, all of which describe the same family of German origin (Olbrich et al. 2002; Olbrich et al. 2006; Loges et al. 2008; Raidt et al. 2014). The p.Arg1454Gln variant was found in a compound heterozygous state with a frameshift variant in two siblings with primary ciliary dyskinesia. The p.Arg1454Gln variant was absent from 200 control chromosomes (Olbrich et al. 2002) and is reported at a frequency of 0.00034 in the African population of the Exome Aggregation Consortium. Direct visualization of respiratory cells from the individuals carrying the variant showed an absence of cilia or membrane alterations. In the remaining ciliated cells, variant DNAH5 was absent from the ciliary axonemes and mislocalized to the basal body region (Olbrich et al. 2006; Loges et al. 2008). The evidence for this variant is limited. The p.Arg1454Gln variant is therefore classified as a variant of unknown significance but suspicious for pathogenicity for primary ciliary dyskinesia. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
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not provided Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at