SLC43A2

protein-coding

solute carrier family 43 member 2, the group of Solute carrier family 43

Gene summary

This gene encodes a member of the L-amino acid transporter-3 or SLC43 family of transporters. The encoded protein mediates sodium-, chloride-, and pH-independent transport of L-isomers of neutral amino acids, including leucine, phenylalanine, valine and methionine. This protein may contribute to the transfer of amino acids across the placental membrane to the fetus. [provided by RefSeq, Mar 2016]

MANE transcript

NM_152346.3

Inheritance

—

ClinVar variants

U:85

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.33

Max pathogenic AF

—

Genomic locus

chr17:1,569,268-1,628,886

External References & Databases

Ensembl (ENSG00000167703)

Transcript & Mutation Effects

hg38 • Region Span ~59.6 kb

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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 SLC43A2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 72

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152346.3. 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			4 clinvar			4
missense			76 clinvar			76
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	85	0	0	85

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 58 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152346.3	RefSeq	NP_689559.1	13	MANE Select
ENST00000301335.10	Ensembl	ENSP00000301335.5	13	MANE Select
NM_001284498.2	RefSeq	NP_001271427.1	14	Standard
NM_001284499.1	RefSeq	NP_001271428.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Biopterin metabolism
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

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 membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000301335
Coding exons: 13
Length: 59620
Individuals with no LoFs: 125717
Homozygous LoFs: 0
Heterozygous LoFs: 22
Defined: 125739
p: 0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.80	261	356	0.732	0.0000224	3665
Missense (PolyPhen)		87	149.42	0.58224		1610
Synonymous	1.17	146	165	0.884	0.0000121	1145
Loss of Function	3.25	9	27.4	0.329	0.00000134	293

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00013	0.00012	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Sodium-, chloride-, and pH-independent high affinity transport of large neutral amino acids. {ECO:0000269|PubMed:15659399}.;

Recessive Scores

pRec: 0.125

Intolerance Scores

LoFtool: 0.403
RVIS EVS: -0.98
RVIS percentile EVS: 8.85

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.210

Gene Damage Prediction

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