NM_022455.5(NSD1):c.4966+15T>C AND Sotos syndrome

Germline classification:: Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:: Dec 3, 2021
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:: RCV003231251.10

Allele description [Variation Report for NM_022455.5(NSD1):c.4966+15T>C]

NM_022455.5(NSD1):c.4966+15T>C

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.4966+15T>C

HGVS:

NC_000005.10:g.177257166T>C
NG_009821.1:g.129088T>C
NM_001365684.2:c.4093+15T>C
NM_001409301.1:c.4966+15T>C
NM_001409302.1:c.4966+15T>C
NM_001409303.1:c.4966+15T>C
NM_001409304.1:c.4546+15T>C
NM_001409305.1:c.4213+15T>C
NM_001409306.1:c.4204+15T>C
NM_001409307.1:c.4204+15T>C
NM_001409308.1:c.4093+15T>C
NM_001409309.1:c.4093+15T>C
NM_022455.5:c.4966+15T>CMANE SELECT
NM_172349.5:c.4093+15T>C
LRG_512t1:c.4966+15T>C
LRG_512:g.129088T>C
NC_000005.9:g.176684167T>C
NC_000005.9:g.176684167T>C
NM_022455.4:c.4966+15T>C

Links:

dbSNP: rs587784130

NCBI 1000 Genomes Browser:

rs587784130

Molecular consequence:

NM_001365684.2:c.4093+15T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001409301.1:c.4966+15T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001409302.1:c.4966+15T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001409303.1:c.4966+15T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001409304.1:c.4546+15T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001409305.1:c.4213+15T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001409306.1:c.4204+15T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001409307.1:c.4204+15T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001409308.1:c.4093+15T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001409309.1:c.4093+15T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_022455.5:c.4966+15T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_172349.5:c.4093+15T>C - intron variant - [Sequence Ontology: SO:0001627]

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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PREDICTED: Homo sapiens 8-oxoguanine DNA glycosylase (OGG1), transcript variant ...
PREDICTED: Homo sapiens 8-oxoguanine DNA glycosylase (OGG1), transcript variant X2, mRNA
gi|2217344064|ref|XM_017006494.3|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000194185	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]
SCV000782183	Center for Human Genetics, Inc, Center for Human Genetics, Inc	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Nov 1, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002055022	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]
SCV002441406	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Dec 3, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

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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
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

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

See all PubMed Citations (3)

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000194185.1

#	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 Center for Human Genetics, Inc, Center for Human Genetics, Inc, SCV000782183.1

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome-Nilou Lab, SCV002055022.1

#	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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002441406.2

#	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

Last Updated: Oct 13, 2024

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