NM_001164277.2(SLC37A4):c.703GTG[1] (p.Val236del) AND Glucose-6-phosphate transport defect

Germline classification:: Likely pathogenic (4 submissions)
Last evaluated:: Dec 9, 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:: RCV000007342.12

Allele description [Variation Report for NM_001164277.2(SLC37A4):c.703GTG[1] (p.Val236del)]

NM_001164277.2(SLC37A4):c.703GTG[1] (p.Val236del)

Gene:

SLC37A4:solute carrier family 37 member 4 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

11q23.3

Genomic location:

Preferred name:

NM_001164277.2(SLC37A4):c.703GTG[1] (p.Val236del)

Other names:

V235del; V235delV

HGVS:

NC_000011.10:g.119027013CAC[1]
NG_013331.1:g.8888GTG[1]
NM_001164277.2:c.703GTG[1]MANE SELECT
NM_001164278.2:c.703GTG[1]
NM_001164279.2:c.484GTG[1]
NM_001164280.2:c.703GTG[1]
NM_001467.6:c.703GTG[1]
NP_001157749.1:p.Val236del
NP_001157750.1:p.Val236del
NP_001157751.1:p.Val163del
NP_001157752.1:p.Val236del
NP_001458.1:p.Val236del
LRG_187:g.8888GTG[1]
NC_000011.10:g.119027013_119027015delCAC
NC_000011.9:g.118897723CAC[1]
NC_000011.9:g.118897723_118897725del
NM_001164277.1:c.706_708del
NM_001164277.2:c.706_708delMANE SELECT

Protein change:

V163del; VAL235DEL

Links:

OMIM: 602671.0010; dbSNP: rs121908977

NCBI 1000 Genomes Browser:

rs121908977

Molecular consequence:

NM_001164277.2:c.703GTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001164278.2:c.703GTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001164279.2:c.484GTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001164280.2:c.703GTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001467.6:c.703GTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Glucose-6-phosphate transport defect (GSD1B)
Synonyms:: Glycogen storage disease type 1B; GSD Ib
Identifiers:: MONDO: MONDO:0009288; MedGen: C0268146; Orphanet: 364; Orphanet: 79259; OMIM: 232220

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000027540	OMIM	no assertion criteria provided	Pathogenic (Sep 17, 1999)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV001392637	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Dec 9, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 34093448, 12444104, 28492532
SCV002517415	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2019)	Likely pathogenic (May 4, 2022)	germline	clinical testing	Citation Link,
SCV004202497	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (May 16, 2022)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

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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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Glycogen storage disease type Ib: structural and mutational analysis of the microsomal glucose-6-phosphate transporter gene.

Hou DC, Kure S, Suzuki Y, Hasegawa Y, Hara Y, Inoue T, Kida Y, Matsubara Y, Narisawa K.

Am J Med Genet. 1999 Sep 17;86(3):253-7.

PubMed [citation]

PMID:: 10482875

Neurological Characteristics of Pediatric Glycogen Storage Disease.

Muzetti JH, do Valle DA, Santos MLSF, Telles BA, Cordeiro ML.

Front Endocrinol (Lausanne). 2021;12:685272. doi: 10.3389/fendo.2021.685272.

PubMed [citation]

PMID:: 34093448
PMCID:: PMC8176209

See all PubMed Citations (5)

Details of each submission

From OMIM, SCV000027540.2

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

Description

In a consanguineous family with GSD Ib (GSD1B; 232220), Hou et al. (1999) identified a 3-bp deletion (val235del) in exon 2 of the G6PT1 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001392637.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant, c.706_708del, results in the deletion of 1 amino acid(s) of the SLC37A4 protein (p.Val236del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with glycogen storage disease (PMID: 34093448; Invitae). This variant is also known as delV235, c.703_705delGTG. ClinVar contains an entry for this variant (Variation ID: 6930). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects SLC37A4 function (PMID: 12444104). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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

From Mendelics, SCV002517415.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

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

From Baylor Genetics, SCV004202497.1

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

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

Last Updated: Sep 29, 2024

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