SLC46A2

solute carrier family 46 member 2, the group of Solute carrier family 46

Basic information

Region (hg38): 9:112878920-112890876

Previous symbols: [ "TSCOT" ]

Links

ENSG00000119457 ∙ NCBI:57864 ∙ OMIM:608956 ∙ HGNC:16055 ∙ Uniprot:Q9BY10 ∙ 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 SLC46A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC46A2 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					3	3
missense			44	2	1	47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	2	4

Variants in SLC46A2

This is a list of pathogenic ClinVar variants found in the SLC46A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-112879775-A-G		not specified	Uncertain significance (Jul 25, 2023)
9-112879788-G-A		not specified	Uncertain significance (Dec 10, 2024)
9-112886473-T-C		not specified	Uncertain significance (Dec 01, 2022)
9-112886499-A-G		not specified	Uncertain significance (Aug 04, 2023)
9-112886520-A-G		not specified	Uncertain significance (Feb 05, 2024)
9-112886605-C-T		not specified	Uncertain significance (Dec 20, 2023)
9-112887338-G-C		not specified	Uncertain significance (Jan 17, 2024)
9-112887410-C-T		not specified	Uncertain significance (Dec 14, 2024)
9-112889555-A-G		not specified	Uncertain significance (Oct 08, 2024)
9-112889576-T-C		not specified	Uncertain significance (Mar 28, 2024)
9-112889585-G-A			Benign (Apr 30, 2018)
9-112889606-C-T		not specified	Uncertain significance (Mar 13, 2023)
9-112889645-C-T		not specified	Likely benign (Sep 21, 2023)
9-112889666-A-G		not specified	Uncertain significance (Mar 06, 2023)
9-112889670-C-T		not specified	Uncertain significance (Nov 17, 2022)
9-112889775-C-A		not specified	Uncertain significance (Oct 03, 2022)
9-112889775-C-T		not specified	Uncertain significance (Jan 19, 2024)
9-112889778-C-T		not specified	Uncertain significance (May 08, 2023)
9-112889783-G-A		not specified	Uncertain significance (Jul 22, 2024)
9-112889792-A-G		not specified	Uncertain significance (Jan 22, 2025)
9-112889811-T-C		not specified	Uncertain significance (Apr 25, 2022)
9-112889840-G-A		not specified	Uncertain significance (Aug 30, 2021)
9-112889861-C-G		not specified	Uncertain significance (Jan 14, 2025)
9-112889888-T-C		not specified	Likely benign (Dec 12, 2023)
9-112889905-A-G			Benign (Apr 30, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC46A2	protein_coding	protein_coding	ENST00000374228	4	11994

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.34e-11	0.0275	125647	0	101	125748	0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.147	285	292	0.976	0.0000164	3011
Missense in Polyphen		112	126.32	0.88661		1349
Synonymous	1.08	120	136	0.882	0.00000840	1076
Loss of Function	-0.297	16	14.8	1.08	7.44e-7	152

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000747	0.000745
Ashkenazi Jewish	0.00	0.00
East Asian	0.000982	0.000979
Finnish	0.000323	0.000323
European (Non-Finnish)	0.000274	0.000273
Middle Eastern	0.000982	0.000979
South Asian	0.000687	0.000686
Other	0.000654	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a transporter. {ECO:0000250}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.468
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.96

Haploinsufficiency Scores

• pHI: 0.135
• hipred: N
• hipred_score: 0.264
• ghis: 0.443

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.168

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc46a2
• Phenotype: immune system phenotype; hematopoietic system phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: T cell homeostasis;regulation of T cell differentiation;thymus development;transmembrane transport;negative regulation of T cell apoptotic process
• Cellular component: plasma membrane;cell surface;integral component of membrane
• Molecular function: symporter activity