SLC47A2

solute carrier family 47 member 2, the group of Solute carrier family 47

Basic information

Region (hg38): 17:19678287-19718979

Links

ENSG00000180638 ∙ NCBI:146802 ∙ OMIM:609833 ∙ HGNC:26439 ∙ Uniprot:Q86VL8 ∙ 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 SLC47A2 gene.

• Inborn genetic diseases (24 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC47A2 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			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	1

Variants in SLC47A2

This is a list of pathogenic ClinVar variants found in the SLC47A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-19678714-G-A		not specified	Uncertain significance (Dec 06, 2022)
17-19678741-G-A		not specified	Uncertain significance (Jun 23, 2021)
17-19678744-G-A		not specified	Likely benign (Dec 20, 2022)
17-19678765-C-T		not specified	Uncertain significance (Feb 28, 2023)
17-19678766-G-A		not specified	Uncertain significance (Feb 21, 2024)
17-19678815-G-A			Likely benign (Sep 01, 2022)
17-19678846-A-C		not specified	Uncertain significance (Oct 10, 2023)
17-19678848-G-C		not specified	Uncertain significance (Jun 16, 2023)
17-19678867-T-G		not specified	Uncertain significance (Jul 19, 2023)
17-19678898-C-G		not specified	Uncertain significance (Aug 22, 2023)
17-19681564-G-A		not specified	Uncertain significance (Sep 20, 2023)
17-19681583-G-T		not specified	Uncertain significance (Jul 28, 2021)
17-19681594-A-T		not specified	Uncertain significance (Mar 13, 2023)
17-19681636-T-G		not specified	Uncertain significance (Jul 19, 2022)
17-19702608-G-C		not specified	Uncertain significance (Jul 07, 2022)
17-19703134-C-T		not specified	Uncertain significance (Mar 06, 2023)
17-19704161-G-C		not specified	Uncertain significance (Dec 06, 2021)
17-19705471-C-A		not specified	Uncertain significance (Jun 21, 2022)
17-19705472-C-A		not specified	Uncertain significance (Jun 21, 2022)
17-19706698-A-G		not specified	Uncertain significance (Apr 13, 2023)
17-19706728-G-C		not specified	Uncertain significance (Jan 05, 2022)
17-19706752-C-T		not specified	Uncertain significance (May 24, 2023)
17-19706758-C-A		not specified	Uncertain significance (May 26, 2022)
17-19708338-T-C		not specified	Uncertain significance (Oct 25, 2023)
17-19708407-A-G		not specified	Uncertain significance (Dec 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC47A2	protein_coding	protein_coding	ENST00000325411	17	40692

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.28e-15	0.132	125578	0	170	125748	0.000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.346	326	344	0.948	0.0000192	3850
Missense in Polyphen		109	116.3	0.93725		1283
Synonymous	0.189	145	148	0.980	0.00000924	1269
Loss of Function	0.970	25	30.8	0.811	0.00000150	333

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00174	0.00174
Ashkenazi Jewish	0.000913	0.000893
East Asian	0.000117	0.000109
Finnish	0.000240	0.000231
European (Non-Finnish)	0.000789	0.000774
Middle Eastern	0.000117	0.000109
South Asian	0.000550	0.000523
Other	0.00124	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Solute transporter for tetraethylammonium (TEA), 1- methyl-4-phenylpyridinium (MPP), cimetidine, N-methylnicotinamide, metformin, creatinine, guanidine, procainamide, topotecan, estrone sulfate, acyclovir, and ganciclovir. Responsible for the secretion of cationic drugs across the brush border membranes. {ECO:0000269|PubMed:16807400, ECO:0000269|PubMed:16996621, ECO:0000269|PubMed:17509534}.
• Pathway: 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: 0.0870

Intolerance Scores

• loftool: 0.967
• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.28

Haploinsufficiency Scores

• pHI: 0.0335
• hipred: N
• hipred_score: 0.112
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.341

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;drug export;transmembrane transport
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: drug transmembrane transporter activity;drug:proton antiporter activity