X-30304562-GTGTGGCCCACATGACTTTATATCTTTGTACAGAGCATTTCCAGCATCATATCATCCATGCTGACTGTGCCGATGATGGGCCTGAAGAACAGTTCAGCAATGACATTGGCATTGATGAATCTCAGCAGGAAAAGGGTACTATTAAGTTCGATGAATCTGTCATGGGGCCCTTGGTGCGTCATCCTGGTGTGTTCACTGAGTATTTGCTGAGTTCCCCACTGGAGTCCCTGAATGTACTTCACGCACTGCAGGCCCGGCACGTCTGGAGGGAGAAAAATCTCTTTGTTATAAAACAGCTCACCACAGAGTCCTTTGCTAGCTTTTTAAAAATAGCCATTTCTGTTTCATCCCAATTAAACAAGACCCAAAGCTTC-CA

Position:

• chrX-30304562-GTGTGGCCCACATGACTTTATATCTTTGTACAGAGCATTTCCAGCATCATATCATCCATGCTGACTGTGCCGATGATGGGCCTGAAGAACAGTTCAGCAATGACATTGGCATTGATGAATCTCAGCAGGAAAAGGGTACTATTAAGTTCGATGAATCTGTCATGGGGCCCTTGGTGCGTCATCCTGGTGTGTTCACTGAGTATTTGCTGAGTTCCCCACTGGAGTCCCTGAATGTACTTCACGCACTGCAGGCCCGGCACGTCTGGAGGGAGAAAAATCTCTTTGTTATAAAACAGCTCACCACAGAGTCCTTTGCTAGCTTTTTAAAAATAGCCATTTCTGTTTCATCCCAATTAAACAAGACCCAAAGCTTC-CA

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_Strong PM2 PP5_Moderate

The NM_000475.5(NR0B1):​c.1169-112_*17delinsTG variant causes a splice acceptor, coding sequence, 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, coding_sequence, 3_prime_UTR, intron
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 1.08

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]

ACMG classification

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 0.4366596 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/exons	MANE	UniProt
NR0B1	NM_000475.5	c.1169-112_*17delinsTG		splice_acceptor_variant, coding_sequence_variant, 3_prime_UTR_variant, intron_variant	2/2	ENST00000378970.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NR0B1	ENST00000378970.5	c.1169-112_*17delinsTG		splice_acceptor_variant, coding_sequence_variant, 3_prime_UTR_variant, intron_variant	2/2	1	NM_000475.5	P1

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

Submissions by phenotype

Congenital adrenal hypoplasia, X-linked Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München

Oct 17, 2017

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1555972632; hg19: chrX-30322679;