NM_022455.5(NSD1):c.3383del (p.Ser1128fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 21, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003126322.3

Allele description [Variation Report for NM_022455.5(NSD1):c.3383del (p.Ser1128fs)]

NM_022455.5(NSD1):c.3383del (p.Ser1128fs)

Gene:

NSD1:nuclear receptor binding SET domain protein 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

5q35.3

Genomic location:

Preferred name:

NM_022455.5(NSD1):c.3383del (p.Ser1128fs)

HGVS:

NC_000005.10:g.177211782del
NG_009821.1:g.83704del
NM_001365684.2:c.2510delC
NM_001409301.1:c.3383delC
NM_001409302.1:c.3383delC
NM_001409303.1:c.3383delC
NM_001409304.1:c.2963delC
NM_001409305.1:c.2630delC
NM_001409306.1:c.2510delC
NM_001409307.1:c.2510delC
NM_001409308.1:c.2510delC
NM_001409309.1:c.2510delC
NM_022455.5:c.3383delMANE SELECT
NM_172349.5:c.2510delC
NP_001352613.1:p.Ser859fs
NP_001352613.2:p.Ser837Phefs
NP_001396230.1:p.Ser1128Phefs
NP_001396231.1:p.Ser1128Phefs
NP_001396232.1:p.Ser1128Phefs
NP_001396233.1:p.Ser988Phefs
NP_001396234.1:p.Ser877Phefs
NP_001396235.1:p.Ser837Phefs
NP_001396236.1:p.Ser837Phefs
NP_001396237.1:p.Ser837Phefs
NP_001396238.1:p.Ser837Phefs
NP_071900.2:p.Ser1128Phefs
NP_071900.2:p.Ser1128fs
NP_758859.1:p.Ser859fs
NP_758859.2:p.Ser837Phefs
LRG_512t1:c.3383del
LRG_512:g.83704del
LRG_512p1:p.Ser1128Phefs
NC_000005.9:g.176638783del
NM_001365684.1:c.2576del
NM_022455.4:c.3383delC
NM_172349.3:c.2576del

Protein change:

S1128fs

Molecular consequence:

NM_001365684.2:c.2510delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409301.1:c.3383delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409302.1:c.3383delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409303.1:c.3383delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409304.1:c.2963delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409305.1:c.2630delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409306.1:c.2510delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409307.1:c.2510delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409308.1:c.2510delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001409309.1:c.2510delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_022455.5:c.3383del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_172349.5:c.2510delC - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003802770	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL CNVClassificationCriteria Aug2020)	Pathogenic (Sep 21, 2022)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003802770

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL CNVClassificationCriteria Aug2020)

Pathogenic
(Sep 21, 2022)

unknown

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Illumina Laboratory Services, Illumina, SCV003802770.1

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

Description

The NSD1 c.3383del (p.Ser1128PhefsTer13) variant results in the deletion of a nucleotide at position c.3383, causing a shift in the protein reading frame that is predicted to result in premature termination of the protein. Loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay is expected. To our knowledge, this variant has not been reported in the peer-reviewed literature. This variant is not found in version 2.1.1 or version 3.1.2 of the Genome Aggregation Database. This variant was identified in a de novo state. Based on the available evidence, the c.3383del (p.Ser1128PhefsTer13) variant is classified as pathogenic for Sotos syndrome.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 9, 2023

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