SLC46A3

solute carrier family 46 member 3, the group of Solute carrier family 46

Basic information

Region (hg38): 13:28700064-28718970

Links

ENSG00000139508 ∙ NCBI:283537 ∙ OMIM:616764 ∙ HGNC:27501 ∙ Uniprot:Q7Z3Q1 ∙ 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 SLC46A3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC46A3 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						0
missense			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	0	0

Variants in SLC46A3

This is a list of pathogenic ClinVar variants found in the SLC46A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-28703944-A-G		not specified	Uncertain significance (Nov 18, 2022)
13-28703956-C-G		not specified	Uncertain significance (Sep 03, 2024)
13-28704000-G-A		not specified	Uncertain significance (Nov 25, 2024)
13-28704049-C-T		not specified	Uncertain significance (Mar 13, 2023)
13-28704055-C-T		Malignant tumor of prostate	Uncertain significance (-)
13-28710761-T-A		not specified	Uncertain significance (Sep 04, 2024)
13-28710775-G-A		not specified	Uncertain significance (Jan 10, 2022)
13-28710798-C-T		not specified	Uncertain significance (Aug 02, 2021)
13-28712704-T-C		not specified	Uncertain significance (Jan 23, 2024)
13-28712712-G-A		not specified	Uncertain significance (Jan 20, 2023)
13-28712809-T-C		not specified	Uncertain significance (Sep 25, 2023)
13-28712929-A-C		not specified	Uncertain significance (Jan 23, 2024)
13-28713009-C-T		EBV-positive nodal T- and NK-cell lymphoma • not specified	Uncertain significance (Jun 18, 2021)
13-28713068-C-G		not specified	Uncertain significance (Jun 07, 2024)
13-28713205-C-G		not specified	Uncertain significance (Jun 10, 2022)
13-28713205-C-T		not specified	Uncertain significance (May 04, 2022)
13-28713234-A-G		not specified	Uncertain significance (Oct 10, 2023)
13-28713270-T-C		not specified	Uncertain significance (Jun 10, 2024)
13-28713273-A-G		not specified	Uncertain significance (Jun 28, 2024)
13-28713291-G-A		not specified	Uncertain significance (Oct 19, 2024)
13-28713313-T-C		not specified	Uncertain significance (Sep 10, 2024)
13-28713319-A-C		not specified	Uncertain significance (Feb 17, 2022)
13-28713324-G-T		not specified	Uncertain significance (Feb 17, 2022)
13-28713399-G-T		not specified	Uncertain significance (Jun 11, 2021)
13-28713460-T-C		not specified	Uncertain significance (Oct 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC46A3	protein_coding	protein_coding	ENST00000380814	6	18907

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.92e-9	0.449	125517	1	230	125748	0.000919

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.485	224	245	0.913	0.0000123	3005
Missense in Polyphen		58	71.004	0.81686		883
Synonymous	1.18	76	90.3	0.842	0.00000490	934
Loss of Function	0.962	15	19.6	0.766	0.00000118	228

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00151	0.00151
Ashkenazi Jewish	0.000696	0.000695
East Asian	0.000545	0.000544
Finnish	0.000140	0.000139
European (Non-Finnish)	0.00115	0.00114
Middle Eastern	0.000545	0.000544
South Asian	0.00113	0.00108
Other	0.000981	0.000978

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.734
• rvis_EVS: 0
• rvis_percentile_EVS: 53.85

Haploinsufficiency Scores

• pHI: 0.150
• hipred: N
• hipred_score: 0.123
• ghis: 0.459

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: Slc46a3
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: biological_process;transmembrane transport
• Cellular component: integral component of membrane;extracellular exosome
• Molecular function: molecular_function