NM_022455.5(NSD1):c.3393C>T (p.Asn1131=) AND Sotos syndrome

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Sep 30, 2022
Review status:: criteria provided, conflicting classifications

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:: RCV003231134.10

Allele description [Variation Report for NM_022455.5(NSD1):c.3393C>T (p.Asn1131=)]

NM_022455.5(NSD1):c.3393C>T (p.Asn1131=)

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.3393C>T (p.Asn1131=)

HGVS:

NC_000005.10:g.177211792C>T
NG_009821.1:g.83714C>T
NM_001365684.2:c.2520C>T
NM_001409301.1:c.3393C>T
NM_001409302.1:c.3393C>T
NM_001409303.1:c.3393C>T
NM_001409304.1:c.2973C>T
NM_001409305.1:c.2640C>T
NM_001409306.1:c.2520C>T
NM_001409307.1:c.2520C>T
NM_001409308.1:c.2520C>T
NM_001409309.1:c.2520C>T
NM_022455.5:c.3393C>TMANE SELECT
NM_172349.5:c.2520C>T
NP_001352613.2:p.Asn840=
NP_001396230.1:p.Asn1131=
NP_001396231.1:p.Asn1131=
NP_001396232.1:p.Asn1131=
NP_001396233.1:p.Asn991=
NP_001396234.1:p.Asn880=
NP_001396235.1:p.Asn840=
NP_001396236.1:p.Asn840=
NP_001396237.1:p.Asn840=
NP_001396238.1:p.Asn840=
NP_071900.2:p.Asn1131=
NP_071900.2:p.Asn1131=
NP_758859.2:p.Asn840=
LRG_512t1:c.3393C>T
LRG_512:g.83714C>T
LRG_512p1:p.Asn1131=
NC_000005.9:g.176638793C>T
NM_022455.4:c.3393C>T
NP_071900.2:p.(=)

Links:

dbSNP: rs150296373

NCBI 1000 Genomes Browser:

rs150296373

Molecular consequence:

NM_001365684.2:c.2520C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001409301.1:c.3393C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001409302.1:c.3393C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001409303.1:c.3393C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001409304.1:c.2973C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001409305.1:c.2640C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001409306.1:c.2520C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001409307.1:c.2520C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001409308.1:c.2520C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001409309.1:c.2520C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_022455.5:c.3393C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_172349.5:c.2520C>T - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV000194137	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2007)	Uncertain significance (Feb 8, 2013)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001001873	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Sep 30, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002055005	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Jul 15, 2021)	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

SCV000194137

Genetic Services Laboratory, University of Chicago

criteria provided, single submitter

(ACMG Guidelines, 2007)

Uncertain significance
(Feb 8, 2013)

germline

clinical testing

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

SCV001001873

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Sep 30, 2022)

germline

clinical testing

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

SCV002055005

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Jul 15, 2021)

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	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.

Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee..

Genet Med. 2008 Apr;10(4):294-300. doi: 10.1097/GIM.0b013e31816b5cae.

PubMed [citation]

PMID:: 18414213

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

See all PubMed Citations (3)

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000194137.1

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001001873.4

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

From Genome-Nilou Lab, SCV002055005.1

#	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

Last Updated: Nov 10, 2024

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