NM_022455.5(NSD1):c.3029A>G (p.Lys1010Arg) AND Sotos syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 19, 2022
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:: RCV003232661.9

Allele description [Variation Report for NM_022455.5(NSD1):c.3029A>G (p.Lys1010Arg)]

NM_022455.5(NSD1):c.3029A>G (p.Lys1010Arg)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

5q35.3

Genomic location:

Preferred name:

NM_022455.5(NSD1):c.3029A>G (p.Lys1010Arg)

HGVS:

NC_000005.10:g.177211428A>G
NG_009821.1:g.83350A>G
NM_001365684.2:c.2156A>G
NM_001409301.1:c.3029A>G
NM_001409302.1:c.3029A>G
NM_001409303.1:c.3029A>G
NM_001409304.1:c.2609A>G
NM_001409305.1:c.2276A>G
NM_001409306.1:c.2156A>G
NM_001409307.1:c.2156A>G
NM_001409308.1:c.2156A>G
NM_001409309.1:c.2156A>G
NM_022455.5:c.3029A>GMANE SELECT
NM_172349.5:c.2156A>G
NP_001352613.1:p.Lys741Arg
NP_001352613.2:p.Lys719Arg
NP_001396230.1:p.Lys1010Arg
NP_001396231.1:p.Lys1010Arg
NP_001396232.1:p.Lys1010Arg
NP_001396233.1:p.Lys870Arg
NP_001396234.1:p.Lys759Arg
NP_001396235.1:p.Lys719Arg
NP_001396236.1:p.Lys719Arg
NP_001396237.1:p.Lys719Arg
NP_001396238.1:p.Lys719Arg
NP_071900.2:p.Lys1010Arg
NP_071900.2:p.Lys1010Arg
NP_758859.1:p.Lys741Arg
NP_758859.2:p.Lys719Arg
LRG_512t1:c.3029A>G
LRG_512:g.83350A>G
LRG_512p1:p.Lys1010Arg
NC_000005.9:g.176638429A>G
NM_001365684.1:c.2222A>G
NM_022455.4:c.3029A>G
NM_172349.3:c.2222A>G

Protein change:

K1010R

Molecular consequence:

NM_001365684.2:c.2156A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409301.1:c.3029A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409302.1:c.3029A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409303.1:c.3029A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409304.1:c.2609A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409305.1:c.2276A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409306.1:c.2156A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409307.1:c.2156A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409308.1:c.2156A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409309.1:c.2156A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_022455.5:c.3029A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_172349.5:c.2156A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Sotos syndrome (SOTOS)
Synonyms:: Sotos' syndrome; Cerebral gigantism; Distinctive facial appearance, overgrowth in childhood, and learning disabilities or delayed development; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0019349; MedGen: C0175695; Orphanet: 821; OMIM: 117550

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RecName: Full=Palmitoyltransferase ZDHHC2; AltName: Full=Acyltransferase ZDHHC2;...
RecName: Full=Palmitoyltransferase ZDHHC2; AltName: Full=Acyltransferase ZDHHC2; AltName: Full=Zinc finger DHHC domain-containing protein 2; Short=DHHC-2
gi|28202094|sp|P59267.1|ZDHC2_MOUSE

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003002927	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 19, 2022)	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

SCV003002927

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 19, 2022)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003002927.1

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

Description

This sequence change replaces lysine, which is basic and polar, with arginine, which is basic and polar, at codon 1010 of the NSD1 protein (p.Lys1010Arg). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with NSD1-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt NSD1 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Nov 10, 2024

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