NM_017739.4(POMGNT1):c.1943dup (p.Glu650fs) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 24, 2021
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:: RCV001797934.1

Allele description [Variation Report for NM_017739.4(POMGNT1):c.1943dup (p.Glu650fs)]

NM_017739.4(POMGNT1):c.1943dup (p.Glu650fs)

Genes:

POMGNT1:protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-) [Gene - OMIM - HGNC]
TSPAN1:tetraspanin 1 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

1p34.1

Genomic location:

Preferred name:

NM_017739.4(POMGNT1):c.1943dup (p.Glu650fs)

HGVS:

NC_000001.11:g.46189314dup
NG_009205.3:g.35996dup
NM_001243766.2:c.1917dup
NM_001290129.2:c.1877dup
NM_001290130.2:c.1514dup
NM_017739.4:c.1943dupMANE SELECT
NP_001230695.2:p.Lys640fs
NP_001277058.2:p.Glu628fs
NP_001277059.2:p.Glu507fs
NP_060209.4:p.Glu650fs
LRG_701t1:c.1917dup
LRG_701t2:c.1943dup
LRG_701:g.35996dup
LRG_701p1:p.Lys640fs
LRG_701p2:p.Glu650fs
NC_000001.10:g.46654986dup
NG_009205.2:g.35996dup
NM_017739.3:c.1943dupC

Protein change:

E507fs

Links:

dbSNP: rs1557668503

NCBI 1000 Genomes Browser:

rs1557668503

Molecular consequence:

NM_001243766.2:c.1917dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001290129.2:c.1877dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001290130.2:c.1514dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_017739.4:c.1943dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002041753	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Nov 24, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002041753

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Nov 24, 2021)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002041753.1

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

Description

Variant summary: POMGNT1 c.1943dupC (p.Glu650GlyfsX37) causes a frameshift which affects the last 10 amino acids and results in an extension of the protein. The variant was absent in 249868 control chromosomes (gnomAD). To our knowledge, no occurrence of c.1943dupC in individuals affected with POMGNT1-related disorders and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. A ClinVar submitter (evaluation after 2014) cites another protein extension variant creating a termination codon downstream of the variant of interest (c.1905delG, p.Lys635AsnfsX58) as likely pathogenic, without providing evidence for independent evaluation (Variation ID: 556807). Three missense and an in-frame duplication variant affecting the last 10 amino acids of the protein (i.e. p.Glu650Lys, p.Pro654Leu, p.Ala656_Glu658dup, p.Thr660Ile) are all cited as VUS in ClinVar. Based on the evidence outlined above, the variant was classified as uncertain significance.

#	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: Dec 24, 2023

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