chr16-70833037-AG-A
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_001270974.2(HYDIN):c.13709del(p.Pro4570LeufsTer22) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 29)
Consequence
HYDIN
NM_001270974.2 frameshift
NM_001270974.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.08
Genes affected
HYDIN (HGNC:19368): (HYDIN axonemal central pair apparatus protein) This gene encodes a protein that may be involved in cilia motility. Mutations in this gene cause of autosomal recessive primary ciliary dyskinesia-5, a disorder characterized by the accumulation of cerebrospinal fluid within the ventricles of the brain. A duplicate copy of this gene has been found in humans on chromosome 1. [provided by RefSeq, Jan 2013]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 16-70833037-AG-A is Pathogenic according to our data. Variant chr16-70833037-AG-A is described in ClinVar as [Pathogenic]. Clinvar id is 3027487.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HYDIN | NM_001270974.2 | c.13709del | p.Pro4570LeufsTer22 | frameshift_variant | 80/86 | ENST00000393567.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HYDIN | ENST00000393567.7 | c.13709del | p.Pro4570LeufsTer22 | frameshift_variant | 80/86 | 5 | NM_001270974.2 | P1 | |
HYDIN | ENST00000378856.8 | c.*2465del | 3_prime_UTR_variant, NMD_transcript_variant | 15/22 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 29
GnomAD3 genomes
?
Cov.:
29
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome ? Cov.: 29
GnomAD4 genome
?
Cov.:
29
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia 5 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Royal Brompton Clinical Genetics And Genomics Laboratory, NHS South East Genomic Laboratory Hub | Mar 06, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.