chr16-67431328-ACCTGCGTCTGGGCCGCCCGCTGCTGGCGGCGCTGGCGCTGCTGGCCGCGCTCGACTGGCTGTGCCAGCGCCTGCTGCCCCCGCCGGCCGCACTCG-A
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_000196.4(HSD11B2):βc.83_177delβ(p.Leu28ArgfsTer32) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000159 in 1,256,246 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (β ).
Frequency
Genomes: π 0.0000067 ( 0 hom., cov: 31)
Exomes π: 9.0e-7 ( 0 hom. )
Consequence
HSD11B2
NM_000196.4 frameshift
NM_000196.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.88
Genes affected
HSD11B2 (HGNC:5209): (hydroxysteroid 11-beta dehydrogenase 2) There are at least two isozymes of the corticosteroid 11-beta-dehydrogenase, a microsomal enzyme complex responsible for the interconversion of cortisol and cortisone. The type I isozyme has both 11-beta-dehydrogenase (cortisol to cortisone) and 11-oxoreductase (cortisone to cortisol) activities. The type II isozyme, encoded by this gene, has only 11-beta-dehydrogenase activity. In aldosterone-selective epithelial tissues such as the kidney, the type II isozyme catalyzes the glucocorticoid cortisol to the inactive metabolite cortisone, thus preventing illicit activation of the mineralocorticoid receptor. In tissues that do not express the mineralocorticoid receptor, such as the placenta and testis, it protects cells from the growth-inhibiting and/or pro-apoptotic effects of cortisol, particularly during embryonic development. Mutations in this gene cause the syndrome of apparent mineralocorticoid excess and hypertension. [provided by RefSeq, Feb 2010]
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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 located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 9 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 16-67431328-ACCTGCGTCTGGGCCGCCCGCTGCTGGCGGCGCTGGCGCTGCTGGCCGCGCTCGACTGGCTGTGCCAGCGCCTGCTGCCCCCGCCGGCCGCACTCG-A is Pathogenic according to our data. Variant chr16-67431328-ACCTGCGTCTGGGCCGCCCGCTGCTGGCGGCGCTGGCGCTGCTGGCCGCGCTCGACTGGCTGTGCCAGCGCCTGCTGCCCCCGCCGGCCGCACTCG-A is described in ClinVar as [Pathogenic]. Clinvar id is 2033856.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HSD11B2 | NM_000196.4 | c.83_177del | p.Leu28ArgfsTer32 | frameshift_variant | 1/5 | ENST00000326152.6 | NP_000187.3 | |
HSD11B2 | XM_047434048.1 | c.-48+552_-48+646del | intron_variant | XP_047290004.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HSD11B2 | ENST00000326152.6 | c.83_177del | p.Leu28ArgfsTer32 | frameshift_variant | 1/5 | 1 | NM_000196.4 | ENSP00000316786 | P1 | |
ENST00000567261.1 | n.42_135+1del | splice_donor_variant, non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000669 AC: 1AN: 149452Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 9.04e-7 AC: 1AN: 1106794Hom.: 0 AF XY: 0.00000185 AC XY: 1AN XY: 539518
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GnomAD4 genome AF: 0.00000669 AC: 1AN: 149452Hom.: 0 Cov.: 31 AF XY: 0.0000137 AC XY: 1AN XY: 72844
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 03, 2022 | For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with HSD11B2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Leu28Argfs*32) in the HSD11B2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in HSD11B2 are known to be pathogenic (PMID: 12860834, 15134813, 17314322). - |
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at