NM_022455.5(NSD1):c.6655del (p.Arg2219fs) AND Neurodevelopmental disorder

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 19, 2020
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:: RCV001374930.1

Allele description [Variation Report for NM_022455.5(NSD1):c.6655del (p.Arg2219fs)]

NM_022455.5(NSD1):c.6655del (p.Arg2219fs)

Gene:

NSD1:nuclear receptor binding SET domain protein 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

5q35.3

Genomic location:

Preferred name:

NM_022455.5(NSD1):c.6655del (p.Arg2219fs)

HGVS:

NC_000005.10:g.177294023del
NG_009821.1:g.165945del
NM_001365684.2:c.5782delC
NM_001409301.1:c.6655delC
NM_001409302.1:c.6655delC
NM_001409303.1:c.6655delC
NM_001409304.1:c.6235delC
NM_001409305.1:c.5902delC
NM_001409306.1:c.5893delC
NM_001409307.1:c.5893delC
NM_001409308.1:c.5782delC
NM_001409309.1:c.5533delC
NM_022455.5:c.6655delMANE SELECT
NM_172349.5:c.5782delC
NP_001352613.1:p.Arg1950fs
NP_001352613.2:p.Arg1928Valfs
NP_001396230.1:p.Arg2219Valfs
NP_001396231.1:p.Arg2219Valfs
NP_001396232.1:p.Arg2219Valfs
NP_001396233.1:p.Arg2079Valfs
NP_001396234.1:p.Arg1968Valfs
NP_001396235.1:p.Arg1965Valfs
NP_001396236.1:p.Arg1965Valfs
NP_001396237.1:p.Arg1928Valfs
NP_001396238.1:p.Arg1845Valfs
NP_071900.2:p.Arg2219Valfs
NP_071900.2:p.Arg2219fs
NP_758859.1:p.Arg1950fs
NP_758859.2:p.Arg1928Valfs
LRG_512t1:c.6655del
LRG_512:g.165945del
NC_000005.9:g.176721024del
NM_001365684.1:c.5848del
NM_022455.4:c.6655del
NM_022455.4:c.6655delC
NM_172349.3:c.5848del

Protein change:

R1950fs

Links:

dbSNP: rs2127279646

NCBI 1000 Genomes Browser:

rs2127279646

Molecular consequence:

NM_001365684.2:c.5782delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409301.1:c.6655delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409302.1:c.6655delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409303.1:c.6655delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409304.1:c.6235delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409305.1:c.5902delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409306.1:c.5893delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409307.1:c.5893delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409308.1:c.5782delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409309.1:c.5533delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_022455.5:c.6655del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_172349.5:c.5782delC - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Neurodevelopmental disorder
Identifiers:: MONDO: MONDO:0700092; MeSH: D065886; MedGen: C1535926

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001572218	Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Feb 19, 2020)	germline	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

SCV001572218

Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Feb 19, 2020)

germline

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	germline	yes	not provided	not provided	not provided	not provided	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 Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes, SCV001572218.1

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

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

Last Updated: Dec 24, 2023

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