chr5-177210713-G-GCAGCAAATCAAGCT

Position:

• chr5-177210713-G-GCAGCAAATCAAGCT

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_022455.5(NSD1):​c.2316_2329dup​(p.Leu777GlnfsTer19) variant causes a frameshift 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 (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: NSD1 NM_022455.5 frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: 0.290

Genes affected

NSD1 (HGNC:14234): (nuclear receptor binding SET domain protein 1) This gene encodes a protein containing a SET domain, 2 LXXLL motifs, 3 nuclear translocation signals (NLSs), 4 plant homeodomain (PHD) finger regions, and a proline-rich region. The encoded protein enhances androgen receptor (AR) transactivation, and this enhancement can be increased further in the presence of other androgen receptor associated coregulators. This protein may act as a nucleus-localized, basic transcriptional factor and also as a bifunctional transcriptional regulator. Mutations of this gene have been associated with Sotos syndrome and Weaver syndrome. One version of childhood acute myeloid leukemia is the result of a cryptic translocation with the breakpoints occurring within nuclear receptor-binding Su-var, enhancer of zeste, and trithorax domain protein 1 on chromosome 5 and nucleoporin, 98-kd on chromosome 11. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Sep 2018]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 5-177210713-G-GCAGCAAATCAAGCT is Pathogenic according to our data. Variant chr5-177210713-G-GCAGCAAATCAAGCT is described in ClinVar as [Pathogenic]. Clinvar id is 407358.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NSD1	NM_022455.5	c.2316_2329dup	p.Leu777GlnfsTer19	frameshift_variant	5/23	ENST00000439151.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NSD1	ENST00000439151.7	c.2316_2329dup	p.Leu777GlnfsTer19	frameshift_variant	5/23	1	NM_022455.5	P2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 37

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, single submitter

Submissions by phenotype

Beckwith-Wiedemann syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 24, 2016

This sequence change inserts 14 nucleotides in exon 5 of the NSD1 mRNA (c.2316_2329dup14), causing a frameshift at codon 777. This creates a premature translational stop signal (p.Leu777Glnfs*19) and is expected to result in an absent or disrupted protein product. While this particular variant has not been reported in the literature, truncating variants in NSD1 are known to be pathogenic (PMID: 12807965, 15942875, 17565729). For these reasons, this variant has been classified as Pathogenic. -

Sotos syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 24, 2016

This sequence change inserts 14 nucleotides in exon 5 of the NSD1 mRNA (c.2316_2329dup14), causing a frameshift at codon 777. This creates a premature translational stop signal (p.Leu777Glnfs*19) and is expected to result in an absent or disrupted protein product. While this particular variant has not been reported in the literature, truncating variants in NSD1 are known to be pathogenic (PMID: 12807965, 15942875, 17565729). For these reasons, this variant has been classified as Pathogenic. -

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: rs1554189490; hg19: chr5-176637714;