SLC47A1

solute carrier family 47 member 1, the group of Solute carrier family 47|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 17:19495384-19579034

Links

ENSG00000142494 ∙ NCBI:55244 ∙ OMIM:609832 ∙ HGNC:25588 ∙ Uniprot:Q96FL8 ∙ 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 SLC47A1 gene.

• Inborn genetic diseases (27 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC47A1 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				1	1	2
missense			24	2	1	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		1	2
Total	0	0	25	3	3

Variants in SLC47A1

This is a list of pathogenic ClinVar variants found in the SLC47A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-19534010-G-T		not specified	Uncertain significance (Aug 01, 2022)
17-19534036-G-A		not specified	Uncertain significance (Jun 11, 2021)
17-19546467-C-T			Benign (Jun 19, 2018)
17-19546468-G-A		not specified	Uncertain significance (Oct 02, 2023)
17-19548018-G-A		not specified	Uncertain significance (May 31, 2023)
17-19548037-C-T		not specified	Uncertain significance (Mar 03, 2022)
17-19548048-C-T		not specified	Uncertain significance (Oct 10, 2023)
17-19548130-C-T		not specified	Uncertain significance (Nov 03, 2023)
17-19555225-C-T		not specified	Uncertain significance (Dec 13, 2022)
17-19555253-C-A		not specified	Uncertain significance (Sep 01, 2021)
17-19555289-T-C			Likely benign (Jun 19, 2018)
17-19555613-T-C		not specified	Uncertain significance (Jul 13, 2021)
17-19555821-C-T			Benign (Feb 20, 2018)
17-19555862-T-C		not specified	Uncertain significance (Mar 29, 2022)
17-19555883-C-T		not specified	Uncertain significance (Feb 16, 2023)
17-19555995-G-T		not specified	Uncertain significance (Aug 08, 2022)
17-19556013-A-T		not specified	Uncertain significance (May 17, 2023)
17-19556018-G-A		not specified	Uncertain significance (Sep 23, 2023)
17-19556030-A-G		not specified	Likely benign (Feb 23, 2023)
17-19556060-A-G		not specified	Uncertain significance (Aug 12, 2022)
17-19560200-T-G		not specified	Uncertain significance (Feb 02, 2022)
17-19560221-C-T		not specified	Uncertain significance (Oct 26, 2021)
17-19560255-A-T		not specified	Uncertain significance (Jan 10, 2022)
17-19560263-C-T		not specified	Uncertain significance (Aug 16, 2022)
17-19560468-G-A		not specified	Uncertain significance (Mar 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC47A1	protein_coding	protein_coding	ENST00000270570	17	83650

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.96e-14	0.108	125671	0	77	125748	0.000306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.186	334	325	1.03	0.0000186	3637
Missense in Polyphen		126	123.41	1.021		1473
Synonymous	-0.392	146	140	1.04	0.00000881	1199
Loss of Function	0.851	24	28.9	0.829	0.00000133	323

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000674	0.000669
Ashkenazi Jewish	0.00	0.00
East Asian	0.000652	0.000653
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000282	0.000281
Middle Eastern	0.000652	0.000653
South Asian	0.000426	0.000425
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Solute transporter for tetraethylammonium (TEA), 1- methyl-4-phenylpyridinium (MPP), cimetidine, N-methylnicotinamide (NMN), metformin, creatinine, guanidine, procainamide, topotecan, estrone sulfate, acyclovir, ganciclovir and also the zwitterionic cephalosporin, cephalexin and cephradin. Seems to also play a role in the uptake of oxaliplatin (a new platinum anticancer agent). Able to transport paraquat (PQ or N,N-dimethyl-4-4'-bipiridinium); a widely used herbicid. Responsible for the secretion of cationic drugs across the brush border membranes. {ECO:0000269|PubMed:16330770, ECO:0000269|PubMed:16996621, ECO:0000269|PubMed:17495125, ECO:0000269|PubMed:17509534, ECO:0000269|PubMed:17582384}.
• Pathway: Metformin Pathway, Pharmacokinetics;Bile salt and organic anion SLC transporters;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules (Consensus)

Recessive Scores

• pRec: 0.0902

Intolerance Scores

• loftool: 0.926
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.6

Haploinsufficiency Scores

• pHI: 0.0653
• hipred: N
• hipred_score: 0.162
• ghis: 0.443

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0769

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc47a2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: drug transmembrane transport;organic cation transport;drug export;transmembrane transport
• Cellular component: plasma membrane;integral component of membrane;vesicle
• Molecular function: drug transmembrane transporter activity;drug:proton antiporter activity