SLC43A1

protein-coding

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

Gene summary

SLC43A1 belongs to the system L family of plasma membrane carrier proteins that transports large neutral amino acids (Babu et al., 2003 [PubMed 12930836]).[supplied by OMIM, Mar 2008]

Previous symbols:

POV1

MANE transcript

NM_003627.6

Inheritance

—

ClinVar variants

U:95B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.47

Max pathogenic AF

—

Genomic locus

chr11:57,484,534-57,515,780

External References & Databases

Ensembl (ENSG00000149150)

Transcript & Mutation Effects

hg38 • Region Span ~31.2 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC43A1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 91

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003627.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	2 clinvar	1 clinvar	5
missense			91 clinvar	5 clinvar	3 clinvar	99
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	95	7	4	106

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 101 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003627.6	RefSeq	NP_003618.1	14	MANE Select
ENST00000278426.8	Ensembl	ENSP00000278426.3	14	MANE Select
NM_001198810.2	RefSeq	NP_001185739.1	14	Standard
ENST00000524995.5	Ensembl	ENSP00000432361.1	2	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
slc43a1a	Danio rerio	Structure: podocyte Quality: increased variability of size abnormal

Gene / Model

Organism

Observed Phenotype

slc43a1a

Danio rerio

Structure: podocyte

Quality: increased variability of size

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

amino acid transport
neutral amino acid transport
L-alpha-amino acid transmembrane transport

Molecular Function

amino acid transmembrane transporter activity
neutral amino acid transmembrane transporter activity
L-amino acid transmembrane transporter activity

Cellular Component

plasma membrane
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000278426
Coding exons: 14
Length: 31253
Individuals with no LoFs: 125681
Homozygous LoFs: 0
Heterozygous LoFs: 67
Defined: 125748
p: 0.000266

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.09	277	333	0.832	0.0000194	3604
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00045	0.00044	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00030	0.00029	rare
South Asian	0.00036	0.00036	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.116

Intolerance Scores

LoFtool: 0.822
RVIS EVS: -0.06
RVIS percentile EVS: 48.84

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0653

Gene Damage Prediction

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