NM_023034.2(NSD3):c.1667C>T (p.Thr556Met) AND not provided

Germline classification:: Likely benign (2 submissions)
Last evaluated:: May 8, 2018
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:: RCV000920252.4

Allele description [Variation Report for NM_023034.2(NSD3):c.1667C>T (p.Thr556Met)]

NM_023034.2(NSD3):c.1667C>T (p.Thr556Met)

Gene:

NSD3:nuclear receptor binding SET domain protein 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8p11.23

Genomic location:

Preferred name:

NM_023034.2(NSD3):c.1667C>T (p.Thr556Met)

HGVS:

NC_000008.11:g.38326771G>A
NG_023292.1:g.60502C>T
NM_017778.3:c.1667C>T
NM_023034.2:c.1667C>TMANE SELECT
NP_060248.2:p.Thr556Met
NP_075447.1:p.Thr556Met
NC_000008.10:g.38184289G>A
NM_023034.1:c.1667C>T

Protein change:

T556M

Links:

dbSNP: rs149768452

NCBI 1000 Genomes Browser:

rs149768452

Molecular consequence:

NM_017778.3:c.1667C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_023034.2:c.1667C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Schizosaccharomyces pombe U3 snoRNP-associated protein Imp4 (imp4), mRNA
Schizosaccharomyces pombe U3 snoRNP-associated protein Imp4 (imp4), mRNA
gi|2745689465|ref|NM_001019214.3|

Nucleotide
inositol polyphosphate phosphatase [Schizosaccharomyces pombe]
inositol polyphosphate phosphatase [Schizosaccharomyces pombe]
gi|19113333|ref|NP_596541.1|

Protein
Mus musculus pancreatic lipase (Pnlip), mRNA
Mus musculus pancreatic lipase (Pnlip), mRNA
gi|1433354059|ref|NM_026925.4|

Nucleotide
Peronospora atriplicis-hastatae isolate 2663 internal transcribed spacer 1, part...
Peronospora atriplicis-hastatae isolate 2663 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
gi|778081676|gb|KP330783.1|

Nucleotide
Homo sapiens cDNA FLJ10604 fis, clone NT2RP2005037, moderately similar to ANTI-S...
Homo sapiens cDNA FLJ10604 fis, clone NT2RP2005037, moderately similar to ANTI-SILENCING PROTEIN 1
gi|7022741|dbj|AK001466.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001065614	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (May 8, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005223406	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign	germline	not provided	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001065614

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(May 8, 2018)

germline

clinical testing

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

SCV005223406

Breakthrough Genomics, Breakthrough Genomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign

germline

not provided

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	not provided
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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001065614.1

#	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 Breakthrough Genomics, Breakthrough Genomics, SCV005223406.1

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

Last Updated: Sep 29, 2024

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