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NM_001164277.2(SLC37A4):c.1042_1043del (p.Leu348fs) AND Glycogen storage disease

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 24, 2017
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:
RCV000601076.11

Allele description [Variation Report for NM_001164277.2(SLC37A4):c.1042_1043del (p.Leu348fs)]

NM_001164277.2(SLC37A4):c.1042_1043del (p.Leu348fs)

Gene:
SLC37A4:solute carrier family 37 member 4 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
11q23.3
Genomic location:
Preferred name:
NM_001164277.2(SLC37A4):c.1042_1043del (p.Leu348fs)
Other names:
1211delCT; p.Leu370ValfsTer53
HGVS:
  • NC_000011.10:g.119025271_119025272del
  • NG_013331.1:g.10634_10635del
  • NM_001164277.2:c.1042_1043delMANE SELECT
  • NM_001164278.2:c.1108_1109del
  • NM_001164279.2:c.823_824del
  • NM_001164280.2:c.1042_1043del
  • NM_001467.6:c.1042_1043del
  • NP_001157749.1:p.Leu348fs
  • NP_001157749.1:p.Leu348fs
  • NP_001157750.1:p.Leu370fs
  • NP_001157751.1:p.Leu275fs
  • NP_001157752.1:p.Leu348fs
  • NP_001458.1:p.Leu348fs
  • LRG_187t1:c.1042_1043del
  • LRG_187:g.10634_10635del
  • LRG_187p1:p.Leu348fs
  • NC_000011.9:g.118895981_118895982del
  • NC_000011.9:g.118895981_118895982delAG
  • NM_001164277.1:c.1042_1043del
  • NM_001164277.1:c.1042_1043delCT
  • NM_001164278.1:c.1108_1109delCT
  • NM_001164278.2:c.1108_1109del
  • NM_001164280.1:c.1042_1043delCT
  • NM_001467.4:c.1042_1043delCT
  • NM_001467.5:c.1042_1043delCT
  • NM_001467.6:c.1042_1043del
  • NP_001458.1:p.Leu348ValfsTer53
  • p.Leu370ValfsX53
Protein change:
L275fs
Links:
OMIM: 602671.0006; dbSNP: rs80356491
NCBI 1000 Genomes Browser:
rs80356491
Molecular consequence:
  • NM_001164277.2:c.1042_1043del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001164278.2:c.1108_1109del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001164279.2:c.823_824del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001164280.2:c.1042_1043del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001467.6:c.1042_1043del - frameshift variant - [Sequence Ontology: SO:0001589]
Functional consequence:
protein truncation [Variation Ontology: 0015]
Observations:
1

Condition(s)

Name:
Glycogen storage disease
Synonyms:
glycogen storage disorder; Disorder of glycogen metabolism
Identifiers:
MONDO: MONDO:0002412; MedGen: C0017919; OMIM: PS232200

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000712814Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)		Pathogenic
(Jan 24, 2017) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided11not providednot providednot providedclinical testing

Citations

PubMed

Molecular diagnosis of type 1c glycogen storage disease.

Janecke AR, Bosshard NU, Mayatepek E, Schulze A, Gitzelmann R, Burchell A, Bartram CR, Janssen B.

Hum Genet. 1999 Mar;104(3):275-7.

PubMed [citation]
PMID:
10323254

Molecular analysis in glycogen storage disease 1 non-A: DHPLC detection of the highly prevalent exon 8 mutations of the G6PT1 gene in German patients.

Santer R, Rischewski J, Block G, Kinner M, Wendel U, Schaub J, Schneppenheim R.

Hum Mutat. 2000 Aug;16(2):177.

PubMed [citation]
PMID:
10923042
See all PubMed Citations (4)

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000712814.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (4)

Description

The p.Leu348ValfsX53 (NM_001164277.1 c.1042_1043delCT) variant in SLC37A4 (also referred to as c.1211delCT in the literature) has been reported in at least 3 ho mozygous and 10 compound heterozygous individuals with clinical features of Glyc ogen storage disease type I (GSDI) (Veiga da Cunha 1998, Janecke 1999, and Sante r 2000). This variant is reported as Pathogenic by three sources in ClinVar (Var iation ID#6926). This variant has also been identified in 13/57880 of European c hromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute .org; dbSNP rs80356491). Although this variant has been seen in the general popu lation, its frequency is low enough to be consistent with a recessive carrier fr equency. This variant is predicted to cause a frameshift, which alters the prote in?s amino acid sequence beginning at position 348 and leads to a premature term ination codon 53 amino acids downstream. This alteration is then predicted to le ad to a truncated or absent protein. Biallelic loss of function of the SLC37A4 gene has been associated with Glycogen storage disease type I (GSDI). In summary , the p.Leu348ValfsX53 variant in SLC37A4 meets criteria for pathogenic for GSDI in an autosomal recessive manner based upon its biallelic occurrence in patient s with this disease and predicted functional impact.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided1not provided1not provided

Last Updated: May 25, 2025