NM_001164277.2(SLC37A4):c.1042_1043del (p.Leu348fs) AND Congenital disorder of glycosylation, type IIw

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 10, 2022
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:: RCV002279712.9

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_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:

Condition(s)

Name:: Congenital disorder of glycosylation, type IIw
Synonyms:: Congenital disorder of glycosylation, type IIw
Identifiers:: MONDO: MONDO:0030437; MedGen: C5561986; OMIM: 619525

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002567981	DASA	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Aug 10, 2022)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 20301489, 28224773, 26913919, 22899091, 15953877, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002567981

DASA

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Aug 10, 2022)

germline

clinical testing

PubMed (6)
[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	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Glycogen Storage Disease Type I.

Bali DS, El-Gharbawy A, Austin S, Pendyal S, Kishnani PS.

2006 Apr 19 [updated 2021 Oct 14]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Bean LJH, Gripp KW, Amemiya A, editors. GeneReviews(®) [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024.

PubMed [citation]

PMID:: 20301489

Novel SLC37A4 Mutations in Korean Patients With Glycogen Storage Disease Ib.

Choi R, Park HD, Ko JM, Lee J, Lee DH, Hong SJ, Ki CS, Lee SY, Kim JW, Song J, Choe YH.

Ann Lab Med. 2017 May;37(3):261-266. doi: 10.3343/alm.2017.37.3.261.

PubMed [citation]

PMID:: 28224773
PMCID:: PMC5339099

See all PubMed Citations (6)

Details of each submission

From DASA, SCV002567981.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (6)

Description

The c.1042_1043del;p.(Leu348Valfs*53) is a null frameshift variant (NMD) in the SLC37A4 gene without sufficient information about prediction of nonsense mediated mRNA decay (NMD); it is present in a relevant exon to the transcript, and disrupts >10% of the protein product – PVS1_strong. This sequence change has been observed in affected individual(s) and ClinVar contains an entry for this variant(Clinvar ID: 6926; PMID: 20301489; 28224773; 26913919; 22899091; 15953877) - PS4. The variant is present at low allele frequencies population databases (rs80356491 – gnomAD 0.002562%; ABraOM 0.002562 frequency - https://abraom.ib.usp.br/) -PM2_supporting.The p.(Leu348Valfs*53) was detected in trans with a pathogenic variant (PMID: 22899091; 26913919; 28224773) - PM3_strong. In summary, the currently available evidence indicates that the variant is pathogenic.

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

Last Updated: Jun 29, 2024

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