NM_173685.4(NSMCE2):c.346del (p.Ser116fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 23, 2023
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:: RCV002523902.3

Allele description [Variation Report for NM_173685.4(NSMCE2):c.346del (p.Ser116fs)]

NM_173685.4(NSMCE2):c.346del (p.Ser116fs)

Gene:

NSMCE2:NSE2 (MMS21) homolog, SMC5-SMC6 complex SUMO ligase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

8q24.13

Genomic location:

Preferred name:

NM_173685.4(NSMCE2):c.346del (p.Ser116fs)

HGVS:

NC_000008.11:g.125182184del
NG_053069.1:g.95367del
NM_001349485.2:c.346del
NM_001349486.2:c.346del
NM_001349487.2:c.346del
NM_173685.4:c.346delMANE SELECT
NP_001336414.1:p.Ser116fs
NP_001336415.1:p.Ser116fs
NP_001336416.1:p.Ser116fs
NP_775956.1:p.Ser116fs
NC_000008.10:g.126194425del
NC_000008.10:g.126194426del
NM_173685.2:c.346del
NR_146191.2:n.691del
NR_146192.2:n.691del

Protein change:

S116fs

Links:

OMIM: 617246.0001; dbSNP: rs757613817

NCBI 1000 Genomes Browser:

rs757613817

Molecular consequence:

NM_001349485.2:c.346del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001349486.2:c.346del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001349487.2:c.346del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_173685.4:c.346del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_146191.2:n.691del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146192.2:n.691del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV003296140	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 23, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 26443207, 25105364, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003296140

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 23, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

NSMCE2 suppresses cancer and aging in mice independently of its SUMO ligase activity.

Jacome A, Gutierrez-Martinez P, Schiavoni F, Tenaglia E, Martinez P, Rodríguez-Acebes S, Lecona E, Murga M, Méndez J, Blasco MA, Fernandez-Capetillo O.

EMBO J. 2015 Nov 3;34(21):2604-19. doi: 10.15252/embj.201591829. Epub 2015 Oct 6.

PubMed [citation]

PMID:: 26443207
PMCID:: PMC4641528

Hypomorphism in human NSMCE2 linked to primordial dwarfism and insulin resistance.

Payne F, Colnaghi R, Rocha N, Seth A, Harris J, Carpenter G, Bottomley WE, Wheeler E, Wong S, Saudek V, Savage D, O'Rahilly S, Carel JC, Barroso I, O'Driscoll M, Semple R.

J Clin Invest. 2014 Sep;124(9):4028-38. doi: 10.1172/JCI73264. Epub 2014 Aug 8.

PubMed [citation]

PMID:: 25105364
PMCID:: PMC4151221

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003296140.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Ser116Leufs*18) in the NSMCE2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NSMCE2 are known to be pathogenic (PMID: 25105364, 26443207). This variant is present in population databases (rs757613817, gnomAD 0.03%). This premature translational stop signal has been observed in individual(s) with clinical features of NSMCE2-related conditions (PMID: 25105364). ClinVar contains an entry for this variant (Variation ID: 372285). For these reasons, this variant has been classified as Pathogenic.

#	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: Sep 29, 2024

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