SLC37A1

protein-coding

solute carrier family 37 member 1, the group of Solute carrier family 37

Gene summary

The protein encoded by this gene localizes to the endoplasmic reticulum (ER) membrane. This protein translocates glucose-6-phosphate from the cytoplasm into the lumen of the ER for hydrolysis into glucose by another ER membrane protein. This gene is a member of the solute carrier 37 gene family. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

MANE transcript

NM_001320537.2

Inheritance

—

ClinVar variants

U:96B:15

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.35

Max pathogenic AF

—

Genomic locus

chr21:42,496,008-42,581,440

External References & Databases

Ensembl (ENSG00000160190)

Transcript & Mutation Effects

hg38 • Region Span ~85.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC37A1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 91

not providedTotal: 17

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001320537.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar		4 clinvar	6
missense			90 clinvar	8 clinvar	3 clinvar	101
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	96	8	7	111

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 88 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001320537.2	RefSeq	NP_001307466.1	19	MANE Select
ENST00000352133.3	Ensembl	ENSP00000344648.2	19	MANE Select
NM_018964.4	RefSeq	NP_061837.3	19	Standard
ENST00000398341.7	Ensembl	ENSP00000381383.3	19	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of carbohydrates
Metabolism
Gluconeogenesis
Glucose metabolism

Biological Process

carbohydrate transport
glucose-6-phosphate transport
phosphate ion transmembrane transport

Molecular Function

glucose 6-phosphate:inorganic phosphate antiporter activity

Cellular Component

endoplasmic reticulum membrane
membrane
integral component of endoplasmic reticulum membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000352133
Coding exons: 19
Length: 85433
Individuals with no LoFs: 125716
Homozygous LoFs: 0
Heterozygous LoFs: 32
Defined: 125748
p: 0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.30	265	332	0.798	0.0000204	3447
Missense (PolyPhen)		124	170.68	0.72649		1759
Synonymous	-0.0290	151	151	1.00	0.0000110	1067
Loss of Function	3.55	12	34.5	0.347	0.00000188	365

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00015	0.00015	rare
South Asian	0.00010	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Inorganic phosphate and glucose-6-phosphate antiporter. May transport cytoplasmic glucose-6-phosphate into the lumen of the endoplasmic reticulum and translocate inorganic phosphate into the opposite direction. Independent of a lumenal glucose-6- phosphatase. May not play a role in homeostatic regulation of blood glucose levels. {ECO:0000269|PubMed:21949678}.;

Recessive Scores

pRec: 0.136

Intolerance Scores

LoFtool: 0.706
RVIS EVS: -0.71
RVIS percentile EVS: 14.71

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.302

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium