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NM_017739.4(POMGNT1):c.698C>T (p.Ser233Phe) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 14, 2016
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:
RCV000413042.1

Allele description [Variation Report for NM_017739.4(POMGNT1):c.698C>T (p.Ser233Phe)]

NM_017739.4(POMGNT1):c.698C>T (p.Ser233Phe)

Genes:
POMGNT1:protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-) [Gene - OMIM - HGNC]
TSPAN1:tetraspanin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p34.1
Genomic location:
Preferred name:
NM_017739.4(POMGNT1):c.698C>T (p.Ser233Phe)
HGVS:
  • NC_000001.11:g.46194606G>A
  • NG_009205.3:g.30700C>T
  • NM_001243766.1:c.698C>T
  • NM_001243766.2:c.698C>T
  • NM_001290129.2:c.632C>T
  • NM_001290130.2:c.269C>T
  • NM_017739.4:c.698C>TMANE SELECT
  • NP_001230695.2:p.Ser233Phe
  • NP_001277058.2:p.Ser211Phe
  • NP_001277059.2:p.Ser90Phe
  • NP_060209.3:p.Ser233Phe
  • NP_060209.4:p.Ser233Phe
  • LRG_701t1:c.698C>T
  • LRG_701t2:c.698C>T
  • LRG_701:g.30700C>T
  • LRG_701p1:p.Ser233Phe
  • LRG_701p2:p.Ser233Phe
  • NC_000001.10:g.46660278G>A
  • NG_009205.2:g.30700C>T
  • NM_017739.3:c.698C>T
Protein change:
S211F
Links:
dbSNP: rs569061665
NCBI 1000 Genomes Browser:
rs569061665
Molecular consequence:
  • NM_001243766.2:c.698C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001290129.2:c.632C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001290130.2:c.269C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_017739.4:c.698C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000492339GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Dec 14, 2016) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000492339.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

A variant of uncertain significance has been identified in the POMGNT1 gene. The S233F variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The S233F variant is observed in 43/16,512 (0.3%) alleles from individuals of South Asian background (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The S233F variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position where amino acids with similar properties to Serine are tolerated across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. Based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 11, 2025