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NM_032520.5(GNPTG):c.67G>C (p.Gly23Arg) AND GNPTG-mucolipidosis

Germline classification:
Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:
Nov 7, 2021
Review status:
criteria provided, conflicting classifications
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:
RCV000407474.10

Allele description [Variation Report for NM_032520.5(GNPTG):c.67G>C (p.Gly23Arg)]

NM_032520.5(GNPTG):c.67G>C (p.Gly23Arg)

Genes:
LOC130058158:ATAC-STARR-seq lymphoblastoid silent region 6972 [Gene]
GNPTG:N-acetylglucosamine-1-phosphate transferase subunit gamma [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
NM_032520.5(GNPTG):c.67G>C (p.Gly23Arg)
HGVS:
  • NC_000016.10:g.1352116G>C
  • NG_016985.1:g.5218G>C
  • NM_032520.5:c.67G>CMANE SELECT
  • NP_115909.1:p.Gly23Arg
  • NC_000016.9:g.1402117G>C
  • NM_032520.4:c.67G>C
Protein change:
G23R
Links:
dbSNP: rs547624231
NCBI 1000 Genomes Browser:
rs547624231
Molecular consequence:
  • NM_032520.5:c.67G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
GNPTG-mucolipidosis
Synonyms:
ML III GAMMA; ML IIIC; MUCOLIPIDOSIS III, COMPLEMENTATION GROUP C; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009652; MedGen: C1854896; Orphanet: 577; OMIM: 252605

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000394859Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)
Uncertain significance
(Jan 12, 2018)
germlineclinical testing

Citation Link,

SCV001457231Natera, Inc.
no assertion criteria provided
Uncertain significance
(Apr 24, 2020)
germlineclinical testing

SCV002045535Genome-Nilou Lab
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely benign
(Nov 7, 2021)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000394859.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

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

From Natera, Inc., SCV001457231.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Genome-Nilou Lab, SCV002045535.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 12, 2024