NM_001164277.2(SLC37A4):c.1125-7_1125-6del AND Glucose-6-phosphate transport defect

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Jan 11, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV000665177.8

Allele description [Variation Report for NM_001164277.2(SLC37A4):c.1125-7_1125-6del]

NM_001164277.2(SLC37A4):c.1125-7_1125-6del

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.1125-7_1125-6del

HGVS:

NC_000011.10:g.119025082_119025083del
NG_013331.1:g.10823_10824del
NM_001164277.2:c.1125-7_1125-6delMANE SELECT
NM_001164278.2:c.1191-7_1191-6del
NM_001164279.2:c.906-7_906-6del
NM_001164280.2:c.1125-7_1125-6del
NM_001467.6:c.1125-7_1125-6del
LRG_187:g.10823_10824del
NC_000011.9:g.118895792_118895793del
NM_001164277.1:c.1124-7_1124-6delCT

Links:

dbSNP: rs782342989

NCBI 1000 Genomes Browser:

rs782342989

Molecular consequence:

NM_001164277.2:c.1125-7_1125-6del - intron variant - [Sequence Ontology: SO:0001627]
NM_001164278.2:c.1191-7_1191-6del - intron variant - [Sequence Ontology: SO:0001627]
NM_001164279.2:c.906-7_906-6del - intron variant - [Sequence Ontology: SO:0001627]
NM_001164280.2:c.1125-7_1125-6del - intron variant - [Sequence Ontology: SO:0001627]
NM_001467.6:c.1125-7_1125-6del - intron variant - [Sequence Ontology: SO:0001627]

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
SCV000789250	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Uncertain significance (Jan 30, 2017)	unknown	clinical testing	Citation Link,
SCV002400763	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 11, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000789250

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Uncertain significance
(Jan 30, 2017)

unknown

clinical testing

Citation Link,

SCV002400763

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 11, 2024)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Counsyl, SCV000789250.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002400763.3

#	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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