NM_001164277.2(SLC37A4):c.1042_1043del (p.Leu348fs) AND Phosphate transport defect

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Feb 23, 2023
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:: RCV000007337.11

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]

Condition(s)

Name:: Phosphate transport defect (GSD1C)
Synonyms:: GLYCOGEN STORAGE DISEASE Ic; GSD Ic
Identifiers:: MedGen: C0342749; Orphanet: 364; Orphanet: 79259; OMIM: 232240

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000027535	OMIM	no assertion criteria provided	Pathogenic (Mar 1, 1999)	germline	literature only	PubMed (2) [See all records that cite these PMIDs] 9758626, 10323254
SCV003841821	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Feb 23, 2023)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 9781688, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000027535

OMIM

no assertion criteria provided

Pathogenic
(Mar 1, 1999)

germline

literature only

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

SCV003841821

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Feb 23, 2023)

unknown

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A gene on chromosome 11q23 coding for a putative glucose- 6-phosphate translocase is mutated in glycogen-storage disease types Ib and Ic.

Veiga-da-Cunha M, Gerin I, Chen YT, de Barsy T, de Lonlay P, Dionisi-Vici C, Fenske CD, Lee PJ, Leonard JV, Maire I, McConkie-Rosell A, Schweitzer S, Vikkula M, Van Schaftingen E.

Am J Hum Genet. 1998 Oct;63(4):976-83.

PubMed [citation]

PMID:: 9758626
PMCID:: PMC1377500

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

See all PubMed Citations (4)

Details of each submission

From OMIM, SCV000027535.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (2)

Description

In 2 families, Veiga-da-Cunha et al. (1998) found that patients with glycogen storage disease Ib (GSD1B; 232220) were homozygous for a 2-bp deletion (1211-1212delCT) in the G6PT1 gene, resulting in a change in reading frame after ala347.

This common frameshift mutation was reported by Veiga-da-Cunha et al. (1998) to be present in 8 GSD Ib patients. In a Turkish patient with GSD Ic (GSD1C; 232240), Janecke et al. (1999) identified the same mutation. Thus, GSD Ib and Ic result from the same mutation of the same gene.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From 3billion, SCV003841821.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.020%). This variant was predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000006926 / PMID: 9781688). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Aug 18, 2024

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