SLC37A1

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

Basic information

Region (hg38): 21:42496007-42581440

Links

ENSG00000160190 ∙ NCBI:54020 ∙ OMIM:608094 ∙ HGNC:11024 ∙ Uniprot:P57057 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC37A1 gene.

• Inborn genetic diseases (31 variants)
• not provided (19 variants)
• Primary ciliary dyskinesia (5 variants)
• Primary ciliary dyskinesia 24 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC37A1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					4	4
missense			28	3	3	34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					4	4
non coding	1		2	10		13
Total	1	0	30	13	7

Variants in SLC37A1

This is a list of pathogenic ClinVar variants found in the SLC37A1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
21-42496126-C-T			Likely benign (Jul 12, 2018)
21-42496148-T-A		Primary ciliary dyskinesia	Uncertain significance (Oct 26, 2020)
21-42496169-C-G		Primary ciliary dyskinesia	Likely benign (Jun 30, 2022)
21-42496176-A-C		Primary ciliary dyskinesia • Inborn genetic diseases	Uncertain significance (Aug 03, 2022)
21-42496181-C-G		Primary ciliary dyskinesia	Likely benign (Oct 16, 2023)
21-42496186-T-G		Primary ciliary dyskinesia	Pathogenic (Jun 04, 2022)
21-42496229-G-A		Primary ciliary dyskinesia 24	Benign (Nov 07, 2021)
21-42518462-G-A		not specified	Likely benign (Feb 28, 2024)
21-42518470-G-A		not specified	Uncertain significance (Jul 20, 2021)
21-42518479-C-T		not specified	Uncertain significance (Mar 02, 2023)
21-42525783-G-A		not specified	Uncertain significance (Mar 24, 2023)
21-42525814-A-G		not specified	Uncertain significance (Jul 30, 2023)
21-42534731-G-A		not specified	Uncertain significance (Sep 16, 2021)
21-42534740-G-A			Benign (Jun 21, 2018)
21-42534776-G-A		not specified	Uncertain significance (Jan 19, 2024)
21-42534785-C-G		not specified	Uncertain significance (Sep 14, 2023)
21-42534809-G-A		not specified	Uncertain significance (Jun 12, 2023)
21-42535534-G-A		not specified	Uncertain significance (Jan 22, 2024)
21-42535543-T-A		not specified	Uncertain significance (Jul 14, 2021)
21-42539528-C-T		not specified	Uncertain significance (Jun 21, 2022)
21-42539529-G-A		not specified	Uncertain significance (Feb 10, 2022)
21-42539564-C-T		not specified	Uncertain significance (Jun 21, 2022)
21-42539566-C-G			Benign (Jul 31, 2018)
21-42539566-C-T			Benign (Jul 20, 2018)
21-42539610-A-G		not specified	Uncertain significance (Oct 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC37A1	protein_coding	protein_coding	ENST00000352133	19	85433

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000581	0.999	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	265	332	0.798	0.0000204	3447
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000418	0.000416
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.00	0.00
South Asian	0.000101	0.0000980
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Metabolism of carbohydrates;Metabolism;Gluconeogenesis;Glucose metabolism (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.706
• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.71

Haploinsufficiency Scores

• pHI: 0.0989
• hipred: Y
• hipred_score: 0.592
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.302

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc37a1

Gene ontology

• Biological process: carbohydrate transport;glucose-6-phosphate transport;phosphate ion transmembrane transport
• Cellular component: endoplasmic reticulum membrane;membrane;integral component of endoplasmic reticulum membrane
• Molecular function: glucose 6-phosphate:inorganic phosphate antiporter activity