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NM_005660.3(SLC35A2):c.947_948del (p.Phe316fs) AND SLC35A2-congenital disorder of glycosylation

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 3, 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:
RCV001063440.8

Allele description [Variation Report for NM_005660.3(SLC35A2):c.947_948del (p.Phe316fs)]

NM_005660.3(SLC35A2):c.947_948del (p.Phe316fs)

Gene:
SLC35A2:solute carrier family 35 member A2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
Xp11.23
Genomic location:
Preferred name:
NM_005660.3(SLC35A2):c.947_948del (p.Phe316fs)
HGVS:
  • NC_000023.11:g.48904962_48904963del
  • NG_015967.1:g.12045_12046del
  • NG_034300.1:g.11997_11998del
  • NM_001032289.3:c.427-70_427-69del
  • NM_001042498.3:c.947_948del
  • NM_001282647.2:c.427-70_427-69del
  • NM_001282648.2:c.355-70_355-69del
  • NM_001282649.2:c.764_765del
  • NM_001282650.2:c.986_987del
  • NM_001282651.2:c.1031_1032del
  • NM_005660.3:c.947_948delMANE SELECT
  • NP_001035963.1:p.Phe316fs
  • NP_001269578.1:p.Phe255fs
  • NP_001269579.1:p.Phe329fs
  • NP_001269580.1:p.Phe344fs
  • NP_005651.1:p.Phe316fs
  • NC_000023.10:g.48762238_48762239del
  • NC_000023.10:g.48762239_48762240del
  • NM_001042498.2:c.947_948del
Protein change:
F255fs
Links:
dbSNP: rs2063477918
NCBI 1000 Genomes Browser:
rs2063477918
Molecular consequence:
  • NM_001042498.3:c.947_948del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001282649.2:c.764_765del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001282650.2:c.986_987del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001282651.2:c.1031_1032del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_005660.3:c.947_948del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001032289.3:c.427-70_427-69del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001282647.2:c.427-70_427-69del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001282648.2:c.355-70_355-69del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
SLC35A2-congenital disorder of glycosylation
Synonyms:
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIm; CDG IIm; CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIm, SOMATIC MOSAIC; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010478; MedGen: C3806688; Orphanet: 356961; OMIM: 300896

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001228286Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Feb 3, 2022) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

De novo mutations in SLC35A2 encoding a UDP-galactose transporter cause early-onset epileptic encephalopathy.

Kodera H, Nakamura K, Osaka H, Maegaki Y, Haginoya K, Mizumoto S, Kato M, Okamoto N, Iai M, Kondo Y, Nishiyama K, Tsurusaki Y, Nakashima M, Miyake N, Hayasaka K, Sugahara K, Yuasa I, Wada Y, Matsumoto N, Saitsu H.

Hum Mutat. 2013 Dec;34(12):1708-14. doi: 10.1002/humu.22446. Epub 2013 Oct 15.

PubMed [citation]
PMID:
24115232

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001228286.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the SLC35A2 protein in which other variant(s) (p.Phe324Leufs*25) have been determined to be pathogenic (PMID: 24115232). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. ClinVar contains an entry for this variant (Variation ID: 857712). This frameshift has been observed in individual(s) with SLC35A2-related conditions (Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change results in a frameshift in the SLC35A2 gene (p.Phe316Trpfs*124). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 78 amino acid(s) of the SLC35A2 protein and extend the protein by 45 additional amino acid residues.

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

Last Updated: Sep 29, 2024