SLC43A1

solute carrier family 43 member 1, the group of Solute carrier family 43

Basic information

Region (hg38): 11:57484533-57515780

Previous symbols: [ "POV1" ]

Links

ENSG00000149150 ∙ NCBI:8501 ∙ OMIM:603733 ∙ HGNC:9225 ∙ Uniprot:O75387 ∙ 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 SLC43A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC43A1 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			38	2	3	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	3	4

Variants in SLC43A1

This is a list of pathogenic ClinVar variants found in the SLC43A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-57485101-C-T		not specified	Uncertain significance (Dec 07, 2023)
11-57485133-G-A		not specified	Uncertain significance (Sep 14, 2022)
11-57485170-G-A		not specified	Uncertain significance (Apr 07, 2023)
11-57485224-G-C		not specified	Uncertain significance (Dec 20, 2023)
11-57487130-C-T		not specified	Uncertain significance (Jul 25, 2023)
11-57487143-C-A		not specified	Uncertain significance (Oct 12, 2022)
11-57487172-T-C		not specified	Uncertain significance (Jan 18, 2022)
11-57487195-G-A		not specified	Uncertain significance (Dec 06, 2022)
11-57488925-T-C		not specified	Uncertain significance (Aug 13, 2021)
11-57489295-C-A		not specified	Uncertain significance (May 23, 2024)
11-57489360-C-T		not specified	Uncertain significance (Dec 27, 2023)
11-57489387-C-T		not specified	Uncertain significance (Apr 18, 2023)
11-57491258-C-T			Benign (Jun 21, 2018)
11-57491271-C-A		not specified	Uncertain significance (Mar 15, 2024)
11-57491278-C-T		not specified	Uncertain significance (Feb 17, 2022)
11-57491282-A-C		not specified	Uncertain significance (May 03, 2023)
11-57491720-C-G			Likely benign (Jun 10, 2018)
11-57491809-G-A		not specified	Uncertain significance (Feb 07, 2023)
11-57491829-G-C		not specified	Uncertain significance (Sep 12, 2023)
11-57491848-G-C		not specified	Uncertain significance (Oct 06, 2021)
11-57491857-C-G		not specified	Uncertain significance (Jul 31, 2023)
11-57494020-G-A		not specified	Uncertain significance (Jun 29, 2022)
11-57494047-C-T		not specified	Uncertain significance (Mar 01, 2023)
11-57494053-C-T		not specified	Uncertain significance (Sep 15, 2021)
11-57494092-C-A		not specified	Uncertain significance (Mar 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC43A1	protein_coding	protein_coding	ENST00000278426	14	31253

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000803	0.996	125681	0	67	125748	0.000266

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	277	333	0.832	0.0000194	3604
Missense in Polyphen		112	140.27	0.79844		1549
Synonymous	0.687	130	140	0.926	0.00000883	1158
Loss of Function	2.56	13	27.5	0.472	0.00000142	287

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000446	0.000446
Ashkenazi Jewish	0.00	0.00
East Asian	0.000445	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000301	0.000290
Middle Eastern	0.000445	0.000435
South Asian	0.000359	0.000359
Other	0.000492	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sodium-independent, high affinity transport of large neutral amino acids. Has narrower substrate selectivity compared to SLC7A5 and SLC7A8 and mainly transports branched-chain amino acids and phenylalanine. Plays a role in the development of human prostate cancer, from prostatic intraepithelial neoplasia to invasive prostate cancer. {ECO:0000269|PubMed:11956097, ECO:0000269|PubMed:12930836, ECO:0000269|PubMed:9255310, ECO:0000269|PubMed:9722952}.
• Pathway: Amino acid transport across the plasma membrane;Amino acid and oligopeptide SLC transporters;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Valine, leucine and isoleucine degradation;Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.822
• rvis_EVS: -0.06
• rvis_percentile_EVS: 48.84

Haploinsufficiency Scores

• pHI: 0.132
• hipred: N
• hipred_score: 0.336
• ghis: 0.390

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0653

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc43a1

Zebrafish Information Network

• Gene name: slc43a1a
• Affected structure: podocyte
• Phenotype tag: abnormal
• Phenotype quality: increased variability of size

Gene ontology

• Biological process: amino acid transport;neutral amino acid transport;L-alpha-amino acid transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: amino acid transmembrane transporter activity;neutral amino acid transmembrane transporter activity;L-amino acid transmembrane transporter activity