NM_000475.5:c.1169-112_*17delGAAGCTTTGGGTCTTGTTTAATTGGGATGAAACAGAAATGGCTATTTTTAAAAAGCTAGCAAAGGACTCTGTGGTGAGCTGTTTTATAACAAAGAGATTTTTCTCCCTCCAGACGTGCCGGGCCTGCAGTGCGTGAAGTACATTCAGGGACTCCAGTGGGGAACTCAGCAAATACTCAGTGAACACACCAGGATGACGCACCAAGGGCCCCATGACAGATTCATCGAACTTAATAGTACCCTTTTCCTGCTGAGATTCATCAATGCCAATGTCATTGCTGAACTGTTCTTCAGGCCCATCATCGGCACAGTCAGCATGGATGATATGATGCTGGAAATGCTCTGTACAAAGATATAAAGTCATGTGGGCCACACinsTG

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate

The NM_000475.5(NR0B1):​c.1173-112_*17delGAAGCTTTGGGTCTTGTTTAATTGGGATGAAACAGAAATGGCTATTTTTAAAAAGCTAGCAAAGGACTCTGTGGTGAGCTGTTTTATAACAAAGAGATTTTTCTCCCTCCAGACGTGCCGGGCCTGCAGTGCGTGAAGTACATTCAGGGACTCCAGTGGGGAACTCAGCAAATACTCAGTGAACACACCAGGATGACGCACCAAGGGCCCCATGACAGATTCATCGAACTTAATAGTACCCTTTTCCTGCTGAGATTCATCAATGCCAATGTCATTGCTGAACTGTTCTTCAGGCCCATCATCGGCACAGTCAGCATGGATGATATGATGCTGGAAATGCTCTGTACAAAGATATAAAGTCATGTGGGCCACACinsTG variant causes a splice acceptor, splice region, 3 prime UTR, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).

Frequency

Genomes: not found (cov: 23)

Consequence

NR0B1
NM_000475.5 splice_acceptor, splice_region, 3_prime_UTR, intron

Scores

Not classified

Clinical Significance

Pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 1.08
Variant links:
Genes affected
NR0B1 (HGNC:7960): (nuclear receptor subfamily 0 group B member 1) This gene encodes a protein that contains a DNA-binding domain. The encoded protein acts as a dominant-negative regulator of transcription which is mediated by the retinoic acid receptor. This protein also functions as an anti-testis gene by acting antagonistically to Sry. Mutations in this gene result in both X-linked congenital adrenal hypoplasia and hypogonadotropic hypogonadism. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 8 ACMG points.

PVS1
Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.4373673 fraction of the gene.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant X-30304562-GTGTGGCCCACATGACTTTATATCTTTGTACAGAGCATTTCCAGCATCATATCATCCATGCTGACTGTGCCGATGATGGGCCTGAAGAACAGTTCAGCAATGACATTGGCATTGATGAATCTCAGCAGGAAAAGGGTACTATTAAGTTCGATGAATCTGTCATGGGGCCCTTGGTGCGTCATCCTGGTGTGTTCACTGAGTATTTGCTGAGTTCCCCACTGGAGTCCCTGAATGTACTTCACGCACTGCAGGCCCGGCACGTCTGGAGGGAGAAAAATCTCTTTGTTATAAAACAGCTCACCACAGAGTCCTTTGCTAGCTTTTTAAAAATAGCCATTTCTGTTTCATCCCAATTAAACAAGACCCAAAGCTTC-CA is Pathogenic according to our data. Variant chrX-30304562-GTGTGGCCCACATGACTTTATATCTTTGTACAGAGCATTTCCAGCATCATATCATCCATGCTGACTGTGCCGATGATGGGCCTGAAGAACAGTTCAGCAATGACATTGGCATTGATGAATCTCAGCAGGAAAAGGGTACTATTAAGTTCGATGAATCTGTCATGGGGCCCTTGGTGCGTCATCCTGGTGTGTTCACTGAGTATTTGCTGAGTTCCCCACTGGAGTCCCTGAATGTACTTCACGCACTGCAGGCCCGGCACGTCTGGAGGGAGAAAAATCTCTTTGTTATAAAACAGCTCACCACAGAGTCCTTTGCTAGCTTTTTAAAAATAGCCATTTCTGTTTCATCCCAATTAAACAAGACCCAAAGCTTC-CA is described in ClinVar as [Pathogenic]. Clinvar id is 444073.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NR0B1NM_000475.5 linkc.1169-112_*17delGAAGCTTTGGGTCTTGTTTAATTGGGATGAAACAGAAATGGCTATTTTTAAAAAGCTAGCAAAGGACTCTGTGGTGAGCTGTTTTATAACAAAGAGATTTTTCTCCCTCCAGACGTGCCGGGCCTGCAGTGCGTGAAGTACATTCAGGGACTCCAGTGGGGAACTCAGCAAATACTCAGTGAACACACCAGGATGACGCACCAAGGGCCCCATGACAGATTCATCGAACTTAATAGTACCCTTTTCCTGCTGAGATTCATCAATGCCAATGTCATTGCTGAACTGTTCTTCAGGCCCATCATCGGCACAGTCAGCATGGATGATATGATGCTGGAAATGCTCTGTACAAAGATATAAAGTCATGTGGGCCACACinsTG p.Asp390fs frameshift_variant, stop_lost, splice_region_variant, synonymous_variant Exon 2 of 2 ENST00000378970.5 NP_000466.2 P51843-1F1D8P4
NR0B1NM_000475.5 linkc.1173-112_*17delGAAGCTTTGGGTCTTGTTTAATTGGGATGAAACAGAAATGGCTATTTTTAAAAAGCTAGCAAAGGACTCTGTGGTGAGCTGTTTTATAACAAAGAGATTTTTCTCCCTCCAGACGTGCCGGGCCTGCAGTGCGTGAAGTACATTCAGGGACTCCAGTGGGGAACTCAGCAAATACTCAGTGAACACACCAGGATGACGCACCAAGGGCCCCATGACAGATTCATCGAACTTAATAGTACCCTTTTCCTGCTGAGATTCATCAATGCCAATGTCATTGCTGAACTGTTCTTCAGGCCCATCATCGGCACAGTCAGCATGGATGATATGATGCTGGAAATGCTCTGTACAAAGATATAAAGTCATGTGGGCCACACinsTG splice_acceptor_variant, splice_region_variant, 3_prime_UTR_variant, intron_variant Exon 2 of 2 ENST00000378970.5 NP_000466.2 P51843-1F1D8P4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NR0B1ENST00000378970.5 linkc.1169-112_*17delGAAGCTTTGGGTCTTGTTTAATTGGGATGAAACAGAAATGGCTATTTTTAAAAAGCTAGCAAAGGACTCTGTGGTGAGCTGTTTTATAACAAAGAGATTTTTCTCCCTCCAGACGTGCCGGGCCTGCAGTGCGTGAAGTACATTCAGGGACTCCAGTGGGGAACTCAGCAAATACTCAGTGAACACACCAGGATGACGCACCAAGGGCCCCATGACAGATTCATCGAACTTAATAGTACCCTTTTCCTGCTGAGATTCATCAATGCCAATGTCATTGCTGAACTGTTCTTCAGGCCCATCATCGGCACAGTCAGCATGGATGATATGATGCTGGAAATGCTCTGTACAAAGATATAAAGTCATGTGGGCCACACinsTG p.Asp390fs frameshift_variant, stop_lost, splice_region_variant, synonymous_variant Exon 2 of 2 1 NM_000475.5 ENSP00000368253.4 P51843-1
NR0B1ENST00000378970 linkc.1173-112_*17delGAAGCTTTGGGTCTTGTTTAATTGGGATGAAACAGAAATGGCTATTTTTAAAAAGCTAGCAAAGGACTCTGTGGTGAGCTGTTTTATAACAAAGAGATTTTTCTCCCTCCAGACGTGCCGGGCCTGCAGTGCGTGAAGTACATTCAGGGACTCCAGTGGGGAACTCAGCAAATACTCAGTGAACACACCAGGATGACGCACCAAGGGCCCCATGACAGATTCATCGAACTTAATAGTACCCTTTTCCTGCTGAGATTCATCAATGCCAATGTCATTGCTGAACTGTTCTTCAGGCCCATCATCGGCACAGTCAGCATGGATGATATGATGCTGGAAATGCTCTGTACAAAGATATAAAGTCATGTGGGCCACACinsTG splice_acceptor_variant, splice_region_variant, 3_prime_UTR_variant, intron_variant Exon 2 of 2 1 NM_000475.5 ENSP00000368253.4 P51843-1

Frequencies

GnomAD3 genomes
Cov.:
23
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
23

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Congenital adrenal hypoplasia, X-linked Pathogenic:1
Oct 17, 2017
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1555972632; hg19: chrX-30322679; API