rs397515414
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PVS1PP5
The NM_001270974.2(HYDIN):c.922A>T(p.Lys308Ter) variant causes a stop gained change. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 23)
Exomes 𝑓: 0.0000019 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
HYDIN
NM_001270974.2 stop_gained
NM_001270974.2 stop_gained
Scores
4
2
1
Clinical Significance
Conservation
PhyloP100: 4.70
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PP5
?
Variant 16-71137272-T-A is Pathogenic according to our data. Variant chr16-71137272-T-A is described in ClinVar as [Pathogenic]. Clinvar id is 39699.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HYDIN | NM_001270974.2 | c.922A>T | p.Lys308Ter | stop_gained | 8/86 | ENST00000393567.7 | |
HYDIN | NM_017558.5 | c.922A>T | p.Lys308Ter | stop_gained | 8/20 | ||
HYDIN | NM_001198542.1 | c.1003A>T | p.Lys335Ter | stop_gained | 8/19 | ||
HYDIN | NM_001198543.1 | c.973A>T | p.Lys325Ter | stop_gained | 8/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HYDIN | ENST00000393567.7 | c.922A>T | p.Lys308Ter | stop_gained | 8/86 | 5 | NM_001270974.2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD3 genomes
?
Cov.:
23
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000185 AC: 1AN: 539810Hom.: 0 Cov.: 6 AF XY: 0.00000348 AC XY: 1AN XY: 287208
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1
AN:
539810
Hom.:
Cov.:
6
AF XY:
AC XY:
1
AN XY:
287208
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? Cov.: 23
GnomAD4 genome
?
Cov.:
23
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia 5 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 05, 2012 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
MutationTaster
Benign
A;A;A;A;A;A;A;A;A
Vest4
ClinPred
D
GERP RS
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at