rs587784225
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_015922.3(NSDHL):c.904del(p.Tyr302ThrfsTer10) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: not found (cov: 24)
Consequence
NSDHL
NM_015922.3 frameshift
NM_015922.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.54
Genes affected
NSDHL (HGNC:13398): (NAD(P) dependent steroid dehydrogenase-like) The protein encoded by this gene is localized in the endoplasmic reticulum and is involved in cholesterol biosynthesis. Mutations in this gene are associated with CHILD syndrome, which is a X-linked dominant disorder of lipid metabolism with disturbed cholesterol biosynthesis, and typically lethal in males. Alternatively spliced transcript variants with differing 5' UTR have been found for this gene. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 4 pathogenic variants in the truncated region.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant X-152868897-CT-C is Pathogenic according to our data. Variant chrX-152868897-CT-C is described in ClinVar as [Pathogenic]. Clinvar id is 159456.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NSDHL | NM_015922.3 | c.904del | p.Tyr302ThrfsTer10 | frameshift_variant | 8/8 | ENST00000370274.8 | |
NSDHL | NM_001129765.2 | c.904del | p.Tyr302ThrfsTer10 | frameshift_variant | 9/9 | ||
NSDHL | XM_017029564.2 | c.952del | p.Tyr318ThrfsTer10 | frameshift_variant | 8/8 | ||
NSDHL | XM_011531178.3 | c.904del | p.Tyr302ThrfsTer10 | frameshift_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NSDHL | ENST00000370274.8 | c.904del | p.Tyr302ThrfsTer10 | frameshift_variant | 8/8 | 1 | NM_015922.3 | P1 | |
NSDHL | ENST00000440023.5 | c.904del | p.Tyr302ThrfsTer10 | frameshift_variant | 9/9 | 5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 24
GnomAD3 genomes
?
Cov.:
24
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome ? Cov.: 24
GnomAD4 genome
?
Cov.:
24
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Child syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 08, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
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