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NM_024312.5(GNPTAB):c.2693del (p.Lys898fs) AND multiple conditions

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
Mar 21, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000673774.5

Allele description [Variation Report for NM_024312.5(GNPTAB):c.2693del (p.Lys898fs)]

NM_024312.5(GNPTAB):c.2693del (p.Lys898fs)

Gene:
GNPTAB:N-acetylglucosamine-1-phosphate transferase subunits alpha and beta [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
12q23.2
Genomic location:
Preferred name:
NM_024312.5(GNPTAB):c.2693del (p.Lys898fs)
HGVS:
  • NC_000012.12:g.101764231del
  • NG_021243.1:g.71644del
  • NM_024312.5:c.2693delMANE SELECT
  • NP_077288.2:p.Lys898fs
  • NC_000012.11:g.102158002del
  • NC_000012.11:g.102158009del
  • NM_024312.4:c.2693delA
  • NM_024312.5:c.2693delAMANE SELECT
Protein change:
K898fs
Links:
dbSNP: rs281864999
NCBI 1000 Genomes Browser:
rs281864999
Molecular consequence:
  • NM_024312.5:c.2693del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Mucolipidosis type II
Synonyms:
ML II ALPHA/BETA; I cell disease; Mucolipidosis 2; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009650; MedGen: C2673377; Orphanet: 576; OMIM: 252500
Name:
Pseudo-Hurler polydystrophy (ML3)
Synonyms:
ML III; ML III ALPHA/BETA; Mucolipidosis type 3A; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0018931; MedGen: C0033788; Orphanet: 577; OMIM: 252600

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000799017Counsyl
criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))
Likely pathogenic
(Apr 4, 2018)
unknownclinical testing

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

Citation Link,

SCV002219883Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Mar 21, 2023)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Mucolipidosis II and III alpha/beta: mutation analysis of 40 Japanese patients showed genotype-phenotype correlation.

Otomo T, Muramatsu T, Yorifuji T, Okuyama T, Nakabayashi H, Fukao T, Ohura T, Yoshino M, Tanaka A, Okamoto N, Inui K, Ozono K, Sakai N.

J Hum Genet. 2009 Mar;54(3):145-51. doi: 10.1038/jhg.2009.3. Epub 2009 Feb 6.

PubMed [citation]
PMID:
19197337

Phenotype and genotype in mucolipidoses II and III alpha/beta: a study of 61 probands.

Cathey SS, Leroy JG, Wood T, Eaves K, Simensen RJ, Kudo M, Stevenson RE, Friez MJ.

J Med Genet. 2010 Jan;47(1):38-48. doi: 10.1136/jmg.2009.067736. Epub 2009 Jul 16.

PubMed [citation]
PMID:
19617216
PMCID:
PMC3712854
See all PubMed Citations (4)

Details of each submission

From Counsyl, SCV000799017.1

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002219883.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 39058). This premature translational stop signal has been observed in individual(s) with mucolipidosis III (PMID: 19197337). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change creates a premature translational stop signal (p.Lys898Serfs*13) in the GNPTAB gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GNPTAB are known to be pathogenic (PMID: 19617216, 25107912).

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

Last Updated: Sep 29, 2024