NM_022455.5(NSD1):c.3090G>T (p.Leu1030Phe) AND not provided

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Mar 25, 2020
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:: RCV000879988.13

Allele description [Variation Report for NM_022455.5(NSD1):c.3090G>T (p.Leu1030Phe)]

NM_022455.5(NSD1):c.3090G>T (p.Leu1030Phe)

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.3090G>T (p.Leu1030Phe)

HGVS:

NC_000005.10:g.177211489G>T
NG_009821.1:g.83411G>T
NM_001365684.2:c.2217G>T
NM_001409301.1:c.3090G>T
NM_001409302.1:c.3090G>T
NM_001409303.1:c.3090G>T
NM_001409304.1:c.2670G>T
NM_001409305.1:c.2337G>T
NM_001409306.1:c.2217G>T
NM_001409307.1:c.2217G>T
NM_001409308.1:c.2217G>T
NM_001409309.1:c.2217G>T
NM_022455.5:c.3090G>TMANE SELECT
NM_172349.5:c.2217G>T
NP_001352613.1:p.Leu761Phe
NP_001352613.2:p.Leu739Phe
NP_001396230.1:p.Leu1030Phe
NP_001396231.1:p.Leu1030Phe
NP_001396232.1:p.Leu1030Phe
NP_001396233.1:p.Leu890Phe
NP_001396234.1:p.Leu779Phe
NP_001396235.1:p.Leu739Phe
NP_001396236.1:p.Leu739Phe
NP_001396237.1:p.Leu739Phe
NP_001396238.1:p.Leu739Phe
NP_071900.2:p.Leu1030Phe
NP_071900.2:p.Leu1030Phe
NP_758859.1:p.Leu761Phe
NP_758859.2:p.Leu739Phe
LRG_512t1:c.3090G>T
LRG_512:g.83411G>T
LRG_512p1:p.Leu1030Phe
NC_000005.9:g.176638490G>T
NM_001365684.1:c.2283G>T
NM_022455.4:c.3090G>T
NM_172349.3:c.2283G>T

Protein change:

L1030F

Links:

dbSNP: rs201860097

NCBI 1000 Genomes Browser:

rs201860097

Molecular consequence:

NM_001365684.2:c.2217G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001409301.1:c.3090G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001409302.1:c.3090G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001409303.1:c.3090G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001409304.1:c.2670G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001409305.1:c.2337G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001409306.1:c.2217G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001409307.1:c.2217G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001409308.1:c.2217G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001409309.1:c.2217G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_022455.5:c.3090G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_172349.5:c.2217G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001023046	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Sep 17, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001783470	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Mar 25, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001023046

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Sep 17, 2017)

germline

clinical testing

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

SCV001783470

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(Mar 25, 2020)

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	yes	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

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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001023046.1

#	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 GeneDx, SCV001783470.1

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

Last Updated: Nov 10, 2024

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