NM_133330.3(NSD2):c.1676_1679del AND Global developmental delay

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 25, 2021
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001779037.10

Allele description [Variation Report for NM_133330.3(NSD2):c.1676_1679del]

NM_133330.3(NSD2):c.1676_1679del

Gene:

NSD2:nuclear receptor binding SET domain protein 2 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

4p16.3

Genomic location:

Preferred name:

NM_133330.3(NSD2):c.1676_1679del

HGVS:

NC_000004.12:g.1938450GA[1]
NG_009269.1:g.72055GA[1]
NM_133330.3:c.1676_1679del
NC_000004.11:g.1940177GA[1]
NM_001042424.2:c.1676_1679del
NM_001042424.2:c.1676_1679delGAGA
NM_001042424.3:c.1676_1679delMANE SELECT
NM_133330.2:c.1676_1679del
NM_133330.2:c.1676_1679delGAGA

Links:

OMIM: 602952.0002; dbSNP: rs1553873247

NCBI 1000 Genomes Browser:

rs1553873247

Molecular consequence:

NM_133330.3:c.1676_1679del - splice acceptor variant - [Sequence Ontology: SO:0001574]

Observations:

Condition(s)

Name:: Global developmental delay (DD)
Identifiers:: MedGen: C0557874; Human Phenotype Ontology: HP:0001263

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002014738	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 25, 2021)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002014738

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Oct 25, 2021)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	yes	1	not provided	not provided	1	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From 3billion, SCV002014738.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)

Description

Frameshift: predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant (PVS1). It is not observed in the gnomAD v2.1.1 dataset (PM2). The variant has been reported to be associated with [GeneName] related disorder (ClinVar ID: VCV000547999.8). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	1	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Oct 20, 2024

ClinVar

Relating variation to medicine