NM_022455.5(NSD1):c.3178C>G (p.Pro1060Ala) AND Sotos syndrome

Germline classification:: Uncertain significance (1 submission)
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:: RCV004547226.1

Allele description [Variation Report for NM_022455.5(NSD1):c.3178C>G (p.Pro1060Ala)]

NM_022455.5(NSD1):c.3178C>G (p.Pro1060Ala)

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.3178C>G (p.Pro1060Ala)

HGVS:

NC_000005.10:g.177211577C>G
NG_009821.1:g.83499C>G
NM_001365684.2:c.2305C>G
NM_001409301.1:c.3178C>G
NM_001409302.1:c.3178C>G
NM_001409303.1:c.3178C>G
NM_001409304.1:c.2758C>G
NM_001409305.1:c.2425C>G
NM_001409306.1:c.2305C>G
NM_001409307.1:c.2305C>G
NM_001409308.1:c.2305C>G
NM_001409309.1:c.2305C>G
NM_022455.5:c.3178C>GMANE SELECT
NM_172349.5:c.2305C>G
NP_001352613.2:p.Pro769Ala
NP_001396230.1:p.Pro1060Ala
NP_001396231.1:p.Pro1060Ala
NP_001396232.1:p.Pro1060Ala
NP_001396233.1:p.Pro920Ala
NP_001396234.1:p.Pro809Ala
NP_001396235.1:p.Pro769Ala
NP_001396236.1:p.Pro769Ala
NP_001396237.1:p.Pro769Ala
NP_001396238.1:p.Pro769Ala
NP_071900.2:p.Pro1060Ala
NP_071900.2:p.Pro1060Ala
NP_758859.2:p.Pro769Ala
LRG_512t1:c.3178C>G
LRG_512:g.83499C>G
LRG_512p1:p.Pro1060Ala
NC_000005.9:g.176638578C>G
NM_022455.4:c.3178C>G

Protein change:

P1060A

Molecular consequence:

NM_001365684.2:c.2305C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409301.1:c.3178C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409302.1:c.3178C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409303.1:c.3178C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409304.1:c.2758C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409305.1:c.2425C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409306.1:c.2305C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409307.1:c.2305C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409308.1:c.2305C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001409309.1:c.2305C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_022455.5:c.3178C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_172349.5:c.2305C>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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005042608	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	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

SCV005042608

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

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 Neuberg Centre For Genomic Medicine, NCGM, SCV005042608.1

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

Description

The missense c.3178C>G p.Pro1060Ala variant in NSD1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.Pro1060Ala variant is novel not in any individuals in gnomAD Exomes and 1000 Genomes. This variant has not been reported to the ClinVar database. The amino acid change p.Pro1060Ala in NSD1 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Pro at position 1060 is changed to a Ala changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as a Variant of Uncertain Significance VUS.

#	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: May 19, 2024

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