NM_022455.5(NSD1):c.3004_3005del (p.Lys1002fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 30, 2019
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:: RCV000627408.10

Allele description [Variation Report for NM_022455.5(NSD1):c.3004_3005del (p.Lys1002fs)]

NM_022455.5(NSD1):c.3004_3005del (p.Lys1002fs)

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.3004_3005del (p.Lys1002fs)

HGVS:

NC_000005.10:g.177211403_177211404del
NG_009821.1:g.83325_83326del
NM_001365684.2:c.2131_2132delAA
NM_001409301.1:c.3004_3005delAA
NM_001409302.1:c.3004_3005delAA
NM_001409303.1:c.3004_3005delAA
NM_001409304.1:c.2584_2585delAA
NM_001409305.1:c.2251_2252delAA
NM_001409306.1:c.2131_2132delAA
NM_001409307.1:c.2131_2132delAA
NM_001409308.1:c.2131_2132delAA
NM_001409309.1:c.2131_2132delAA
NM_022455.5:c.3004_3005delMANE SELECT
NM_172349.5:c.2131_2132delAA
NP_001352613.1:p.Lys733fs
NP_001352613.2:p.Lys711Glufs
NP_001396230.1:p.Lys1002Glufs
NP_001396231.1:p.Lys1002Glufs
NP_001396232.1:p.Lys1002Glufs
NP_001396233.1:p.Lys862Glufs
NP_001396234.1:p.Lys751Glufs
NP_001396235.1:p.Lys711Glufs
NP_001396236.1:p.Lys711Glufs
NP_001396237.1:p.Lys711Glufs
NP_001396238.1:p.Lys711Glufs
NP_071900.2:p.Lys1002Glufs
NP_071900.2:p.Lys1002fs
NP_758859.1:p.Lys733fs
NP_758859.2:p.Lys711Glufs
LRG_512t1:c.3004_3005del
LRG_512:g.83325_83326del
LRG_512p1:p.Lys1002Glufs
NC_000005.9:g.176638404_176638405del
NM_001365684.1:c.2197_2198del
NM_022455.4:c.3004_3005delAA
NM_022455.4:c.3004_3005delAA
NM_172349.3:c.2197_2198del

Protein change:

K733fs

Links:

dbSNP: rs1554189941

NCBI 1000 Genomes Browser:

rs1554189941

Molecular consequence:

NM_001365684.2:c.2131_2132delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409301.1:c.3004_3005delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409302.1:c.3004_3005delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409303.1:c.3004_3005delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409304.1:c.2584_2585delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409305.1:c.2251_2252delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409306.1:c.2131_2132delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409307.1:c.2131_2132delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409308.1:c.2131_2132delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409309.1:c.2131_2132delAA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_022455.5:c.3004_3005del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_172349.5:c.2131_2132delAA - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000748403	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Oct 30, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000748403

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Oct 30, 2019)

germline

clinical testing

Citation Link

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

Details of each submission

From GeneDx, SCV000748403.3

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

Description

Reported previously in an individual with Sotos syndrome, as well as in an individual with overgrowth and intellectual disability (Kotilainen et al., 2009; Tatton-Brown et al., 2017); Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 30719864, 19876911, 28475857)

#	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: Nov 24, 2024

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