rs121909833
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4_SupportingPP5
The NM_015922.3(NSDHL):c.696_698del(p.Lys232del) variant causes a inframe deletion change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 23)
Consequence
NSDHL
NM_015922.3 inframe_deletion
NM_015922.3 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.98
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Nonframeshift variant in NON repetitive region in NM_015922.3. Strenght limited to Supporting due to length of the change: 1aa.
PP5
?
Variant X-152867576-GGAA-G is Pathogenic according to our data. Variant chrX-152867576-GGAA-G is described in ClinVar as [Pathogenic]. Clinvar id is 21268.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NSDHL | NM_015922.3 | c.696_698del | p.Lys232del | inframe_deletion | 7/8 | ENST00000370274.8 | |
NSDHL | NM_001129765.2 | c.696_698del | p.Lys232del | inframe_deletion | 8/9 | ||
NSDHL | XM_011531178.3 | c.696_698del | p.Lys232del | inframe_deletion | 9/10 | ||
NSDHL | XM_017029564.2 | c.744_746del | p.Lys248del | inframe_deletion | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NSDHL | ENST00000370274.8 | c.696_698del | p.Lys232del | inframe_deletion | 7/8 | 1 | NM_015922.3 | P1 | |
NSDHL | ENST00000432467.1 | c.696_698del | p.Lys232del | inframe_deletion | 8/8 | 3 | |||
NSDHL | ENST00000440023.5 | c.696_698del | p.Lys232del | inframe_deletion | 8/9 | 5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD3 genomes
?
Cov.:
23
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 23
GnomAD4 genome
?
Cov.:
23
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
CK syndrome Pathogenic:1Other:1
not provided, no classification provided | clinical testing | GeneReviews | - | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 10, 2010 | - - |
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