NM_001164277.2(SLC37A4):c.1042_1043del (p.Leu348fs) AND not provided

Germline classification:: Pathogenic (4 submissions)
Last evaluated:: May 3, 2024
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:: RCV000723824.33

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:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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6-Methyluracil (1)
ClinVar
Mus musculus C-C motif chemokine ligand 27A (Ccl27a), transcript variant 1, mRNA
Mus musculus C-C motif chemokine ligand 27A (Ccl27a), transcript variant 1, mRNA
gi|1358101491|ref|NM_001048179.2|

Nucleotide
PREDICTED: Mus musculus C-C motif chemokine ligand 27A (Ccl27a), transcript vari...
PREDICTED: Mus musculus C-C motif chemokine ligand 27A (Ccl27a), transcript variant X2, mRNA
gi|1907155230|ref|XM_011249967.4|

Nucleotide
Letharia vulpina voucher SNC749 small subunit ribosomal RNA gene, partial sequen...
Letharia vulpina voucher SNC749 small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1 and 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
gi|2499727451|gb|OQ917235.1|

Nucleotide
Psychosis and schizophrenia in children and young people: recognition and manage...
Psychosis and schizophrenia in children and young people: recognition and management

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000331530	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL ClinVar v180209 classification definitions)	Pathogenic (Jul 2, 2018)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 10482962, 10923042 Citation Link,
SCV001168625	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (May 3, 2024)	germline	clinical testing	Citation Link,
SCV002063016	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Dec 1, 2021)	germline	clinical testing	Citation Link,
SCV003821186	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 22, 2021)	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	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	2	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

The putative glucose 6-phosphate translocase gene is mutated in essentially all cases of glycogen storage disease type I non-a.

Veiga-da-Cunha M, Gerin I, Chen YT, Lee PJ, Leonard JV, Maire I, Wendel U, Vikkula M, Van Schaftingen E.

Eur J Hum Genet. 1999 Sep;7(6):717-23.

PubMed [citation]

PMID:: 10482962

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 (3)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000331530.4

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

#	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		2	not provided	not provided	not provided

From GeneDx, SCV001168625.4

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

Description

Frameshift variant predicted to result in abnormal protein length as the last 82 amino acids are replaced with 52 different amino acids, and other similar variants have been reported in HGMD; This variant is associated with the following publications: (PMID: 18437526, 30609409, 31508908, 37147621, 34946936, 34775139, 25971127, 15953877, 9758626, 9781688, 32005221, 31536830, 34426522, 34093448, 31589614, 33977030, 35433171, 35822097, 38087503, 37275680, 38531056, 35620924, 38605407, 36964972, 36039216, 37779861, 10323254)

#	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		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV002063016.18

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

From Revvity Omics, Revvity, SCV003821186.2

#	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 16, 2024

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