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NM_018389.5(SLC35C1):c.260T>C (p.Leu87Pro) AND Leukocyte adhesion deficiency type II

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 16, 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:
RCV002037619.6

Allele description [Variation Report for NM_018389.5(SLC35C1):c.260T>C (p.Leu87Pro)]

NM_018389.5(SLC35C1):c.260T>C (p.Leu87Pro)

Gene:
SLC35C1:solute carrier family 35 member C1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p11.2
Genomic location:
Preferred name:
NM_018389.5(SLC35C1):c.260T>C (p.Leu87Pro)
HGVS:
  • NC_000011.10:g.45806061T>C
  • NG_009875.1:g.6990T>C
  • NM_001145265.2:c.221T>C
  • NM_001145266.2:c.221T>C
  • NM_018389.5:c.260T>CMANE SELECT
  • NP_001138737.1:p.Leu74Pro
  • NP_001138738.1:p.Leu74Pro
  • NP_001138738.1:p.Leu74Pro
  • NP_060859.4:p.Leu87Pro
  • NP_060859.4:p.Leu87Pro
  • LRG_107t1:c.260T>C
  • LRG_107:g.6990T>C
  • LRG_107p1:p.Leu87Pro
  • NC_000011.9:g.45827612T>C
  • NM_001145266.1:c.221T>C
  • NM_018389.4:c.260T>C
Protein change:
L74P
Links:
dbSNP: rs2134590175
NCBI 1000 Genomes Browser:
rs2134590175
Molecular consequence:
  • NM_001145265.2:c.221T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001145266.2:c.221T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_018389.5:c.260T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Leukocyte adhesion deficiency type II
Synonyms:
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIc; CDG IIc; Congenital disorder of glycosylation type 2C; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009953; MedGen: C0398739; Orphanet: 2968; Orphanet: 99843; OMIM: 266265

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002108114Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Apr 16, 2021) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

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, SCV002108114.3

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with SLC35C1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces leucine with proline at codon 87 of the SLC35C1 protein (p.Leu87Pro). The leucine residue is moderately conserved and there is a moderate physicochemical difference between leucine and proline.

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

Last Updated: Sep 29, 2024