NM_022455.5(NSD1):c.3215G>A (p.Arg1072Gln) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (5 submissions)
Last evaluated:: Nov 1, 2023
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:: RCV001573572.25

Allele description [Variation Report for NM_022455.5(NSD1):c.3215G>A (p.Arg1072Gln)]

NM_022455.5(NSD1):c.3215G>A (p.Arg1072Gln)

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.3215G>A (p.Arg1072Gln)

HGVS:

NC_000005.10:g.177211614G>A
NG_009821.1:g.83536G>A
NM_001365684.2:c.2342G>A
NM_001409301.1:c.3215G>A
NM_001409302.1:c.3215G>A
NM_001409303.1:c.3215G>A
NM_001409304.1:c.2795G>A
NM_001409305.1:c.2462G>A
NM_001409306.1:c.2342G>A
NM_001409307.1:c.2342G>A
NM_001409308.1:c.2342G>A
NM_001409309.1:c.2342G>A
NM_022455.5:c.3215G>AMANE SELECT
NM_172349.5:c.2342G>A
NP_001352613.1:p.Arg803Gln
NP_001352613.2:p.Arg781Gln
NP_001396230.1:p.Arg1072Gln
NP_001396231.1:p.Arg1072Gln
NP_001396232.1:p.Arg1072Gln
NP_001396233.1:p.Arg932Gln
NP_001396234.1:p.Arg821Gln
NP_001396235.1:p.Arg781Gln
NP_001396236.1:p.Arg781Gln
NP_001396237.1:p.Arg781Gln
NP_001396238.1:p.Arg781Gln
NP_071900.2:p.Arg1072Gln
NP_071900.2:p.Arg1072Gln
NP_758859.1:p.Arg803Gln
NP_758859.2:p.Arg781Gln
LRG_512t1:c.3215G>A
LRG_512:g.83536G>A
LRG_512p1:p.Arg1072Gln
NC_000005.9:g.176638615G>A
NM_001365684.1:c.2408G>A
NM_022455.4:c.3215G>A
NM_172349.3:c.2408G>A

Protein change:

R1072Q

Links:

dbSNP: rs28932180

NCBI 1000 Genomes Browser:

rs28932180

Molecular consequence:

NM_001365684.2:c.2342G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001409301.1:c.3215G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001409302.1:c.3215G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001409303.1:c.3215G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001409304.1:c.2795G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001409305.1:c.2462G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001409306.1:c.2342G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001409307.1:c.2342G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001409308.1:c.2342G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001409309.1:c.2342G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_022455.5:c.3215G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_172349.5:c.2342G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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
SCV000617890	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Dec 2, 2019)	germline	clinical testing	Citation Link,
SCV001799641	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus	no assertion criteria provided	Likely benign	germline	clinical testing
SCV001974411	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing
SCV002011045	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Nov 3, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004158078	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Nov 1, 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	yes	2	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	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 GeneDx, SCV000617890.3

#	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

From Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus, SCV001799641.1

#	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

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001974411.1

#	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

From Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden, SCV002011045.3

#	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	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV004158078.10

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	not provided

Description

NSD1: BP4

#	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		2	not provided	not provided	not provided

Last Updated: Oct 26, 2024

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