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NM_032520.5(GNPTG):c.29T>A (p.Leu10Ter) AND GNPTG-mucolipidosis

Germline classification:
Conflicting interpretations of pathogenicity (2 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:
RCV000673912.5

Allele description [Variation Report for NM_032520.5(GNPTG):c.29T>A (p.Leu10Ter)]

NM_032520.5(GNPTG):c.29T>A (p.Leu10Ter)

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.29T>A (p.Leu10Ter)
HGVS:
  • NC_000016.10:g.1351994T>A
  • NG_016985.1:g.5096T>A
  • NM_032520.5:c.29T>AMANE SELECT
  • NP_115909.1:p.Leu10Ter
  • NC_000016.9:g.1401995T>A
  • NM_032520.4:c.29T>A
Protein change:
L10*
Links:
dbSNP: rs1555450681
NCBI 1000 Genomes Browser:
rs1555450681
Molecular consequence:
  • NM_032520.5:c.29T>A - nonsense - [Sequence Ontology: SO:0001587]

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
SCV000799168Counsyl
criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))
Uncertain significance
(Apr 12, 2018)
unknownclinical testing

Citation Link,

SCV002045533Genome-Nilou Lab
criteria provided, single submitter

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

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot 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 Counsyl, SCV000799168.1

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

From Genome-Nilou Lab, SCV002045533.1

#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: Sep 29, 2024