NM_001164277.2(SLC37A4):c.217C>T (p.Gln73Ter) AND Glucose-6-phosphate transport defect

Clinical significance:Pathogenic (Last evaluated: Sep 21, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV001174784.2

Allele description [Variation Report for NM_001164277.2(SLC37A4):c.217C>T (p.Gln73Ter)]

NM_001164277.2(SLC37A4):c.217C>T (p.Gln73Ter)

Gene:
SLC37A4:solute carrier family 37 member 4 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q23.3
Genomic location:
Preferred name:
NM_001164277.2(SLC37A4):c.217C>T (p.Gln73Ter)
HGVS:
  • NC_000011.10:g.119028358G>A
  • NG_013331.1:g.7549C>T
  • NM_001164277.1:c.217C>T
  • NM_001164277.2:c.217C>T
  • NM_001164278.2:c.217C>T
  • NM_001164279.2:c.-3C>T
  • NM_001164280.2:c.217C>T
  • NM_001467.6:c.217C>T
  • NP_001157749.1:p.Gln73Ter
  • NP_001157749.1:p.Gln73Ter
  • NP_001157750.1:p.Gln73Ter
  • NP_001157752.1:p.Gln73Ter
  • NP_001458.1:p.Gln73Ter
  • LRG_187t1:c.217C>T
  • LRG_187:g.7549C>T
  • LRG_187p1:p.Gln73Ter
  • NC_000011.9:g.118899068G>A
Protein change:
Q73*
Molecular consequence:
  • NM_001164279.2:c.-3C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001164277.1:c.217C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001164277.2:c.217C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001164278.2:c.217C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001164280.2:c.217C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001467.6:c.217C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Glucose-6-phosphate transport defect (GSD1B)
Synonyms:
Glycogen storage disease type 1B; GSD Ib
Identifiers:
MedGen: C0268146; Orphanet: 364; Orphanet: 79259; OMIM: 232220

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001338118Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Pathogenic
(Jan 27, 2020)
germlineclinical testing

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

Citation Link,

SCV001578029Invitaecriteria provided, single submitter
Pathogenic
(Sep 21, 2020)
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

Citations

PubMed

The SLC37 family of sugar-phosphate/phosphate exchangers.

Chou JY, Mansfield BC.

Curr Top Membr. 2014;73:357-82. doi: 10.1016/B978-0-12-800223-0.00010-4. Review.

PubMed [citation]
PMID:
24745989
PMCID:
PMC4180117

Genetic testing of glycogen storage disease type Ib in Japan: five novel G6PT1 mutations and a rapid detection method for a prevalent mutation W118R.

Kojima K, Kure S, Kamada F, Hao K, Ichinohe A, Sato K, Aoki Y, Yoichi S, Kubota M, Horikawa R, Utsumi A, Miura M, Ogawa S, Kanazawa M, Kohno Y, Inokuchi M, Hasegawa T, Narisawa K, Matsubara Y.

Mol Genet Metab. 2004 Apr;81(4):343-6.

PubMed [citation]
PMID:
15059622
See all PubMed Citations (5)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001338118.1

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

Description

Variant summary: SLC37A4 c.217C>T (p.Gln73X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant was absent in 235820 control chromosomes. c.217C>T has been reported in the literature in at-least one homozygous individual of Japanese ethnicity affected with Glycogen Storage Disease Type Ib (example, Kojima_2004) and has been subsequently cited by others (example, Chou_2014). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as pathogenic.

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

From Invitae, SCV001578029.1

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

Description

This sequence change creates a premature translational stop signal (p.Gln73*) in the SLC37A4 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) SLC37A4-related conditions (PMID: 15059622). ClinVar contains an entry for this variant (Variation ID: 917662). Loss-of-function variants in SLC37A4 are known to be pathogenic (PMID: 9758626, 10940311). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Oct 30, 2021

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