NM_022455.5(NSD1):c.1690G>T (p.Ala564Ser) AND Sotos syndrome

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Sep 18, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV003231174.10

Allele description [Variation Report for NM_022455.5(NSD1):c.1690G>T (p.Ala564Ser)]

NM_022455.5(NSD1):c.1690G>T (p.Ala564Ser)

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.1690G>T (p.Ala564Ser)

HGVS:

NC_000005.10:g.177210089G>T
NG_009821.1:g.82011G>T
NM_001365684.2:c.817G>T
NM_001409301.1:c.1690G>T
NM_001409302.1:c.1690G>T
NM_001409303.1:c.1690G>T
NM_001409304.1:c.1270G>T
NM_001409305.1:c.937G>T
NM_001409306.1:c.817G>T
NM_001409307.1:c.817G>T
NM_001409308.1:c.817G>T
NM_001409309.1:c.817G>T
NM_022455.5:c.1690G>TMANE SELECT
NM_172349.5:c.817G>T
NP_001352613.1:p.Ala295Ser
NP_001352613.2:p.Ala273Ser
NP_001396230.1:p.Ala564Ser
NP_001396231.1:p.Ala564Ser
NP_001396232.1:p.Ala564Ser
NP_001396233.1:p.Ala424Ser
NP_001396234.1:p.Ala313Ser
NP_001396235.1:p.Ala273Ser
NP_001396236.1:p.Ala273Ser
NP_001396237.1:p.Ala273Ser
NP_001396238.1:p.Ala273Ser
NP_071900.2:p.Ala564Ser
NP_071900.2:p.Ala564Ser
NP_758859.1:p.Ala295Ser
NP_758859.2:p.Ala273Ser
LRG_512t1:c.1690G>T
LRG_512:g.82011G>T
LRG_512p1:p.Ala564Ser
NC_000005.9:g.176637090G>T
NM_001365684.1:c.883G>T
NM_022455.4:c.1690G>T
NM_172349.3:c.883G>T

Protein change:

A273S

Links:

dbSNP: rs116520623

Molecular consequence:

NM_001365684.2:c.817G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001409301.1:c.1690G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001409302.1:c.1690G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001409303.1:c.1690G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001409304.1:c.1270G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001409305.1:c.937G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001409306.1:c.817G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001409307.1:c.817G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001409308.1:c.817G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001409309.1:c.817G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_022455.5:c.1690G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_172349.5:c.817G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Sotos syndrome (SOTOS)
Synonyms:: Sotos' syndrome; Distinctive facial appearance, overgrowth in childhood, and learning disabilities or delayed development; CHROMOSOME 5q35 DELETION SYNDROME; 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
SCV002054844	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jul 15, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002799847	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Aug 17, 2021)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004564661	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Benign (Sep 18, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002054844

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Jul 15, 2021)

germline

clinical testing

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

SCV002799847

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Aug 17, 2021)

unknown

clinical testing

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

SCV004564661

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)

Benign
(Sep 18, 2023)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	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 Genome-Nilou Lab, SCV002054844.1

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Fulgent Genetics, Fulgent Genetics, SCV002799847.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV004564661.1

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

#	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: Feb 15, 2026

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