SLC43A1

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

Basic information

Region (hg38): 11:57484534-57515780

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.

not_specified (81 variants)
not_provided (7 variants)

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. These statistics are base on transcript: NM_000003627.6. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	2 clinvar	1 clinvar	5
missense			82 clinvar	4 clinvar	3 clinvar	89
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	86	6	4

Loading clinvar variants...

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
Phenotype

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