SLC43A2

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

Basic information

Region (hg38): 17:1569268-1628886

Links

ENSG00000167703 ∙ NCBI:124935 ∙ OMIM:610791 ∙ HGNC:23087 ∙ Uniprot:Q8N370 ∙ 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 SLC43A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC43A2 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			34			34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	34	0	1

Variants in SLC43A2

This is a list of pathogenic ClinVar variants found in the SLC43A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-1575633-C-T		not specified	Uncertain significance (Jan 31, 2022)
17-1575654-T-C		not specified	Uncertain significance (Apr 24, 2024)
17-1575683-C-A		not specified	Uncertain significance (Dec 17, 2023)
17-1575695-C-T		not specified	Uncertain significance (Apr 24, 2024)
17-1575747-G-A		not specified	Uncertain significance (Dec 09, 2023)
17-1575759-C-T		not specified	Uncertain significance (Aug 17, 2022)
17-1576607-T-C		not specified	Uncertain significance (May 02, 2024)
17-1576631-G-A		not specified	Uncertain significance (Oct 06, 2022)
17-1576644-G-T		not specified	Uncertain significance (May 11, 2022)
17-1583259-T-C		not specified	Uncertain significance (Nov 08, 2022)
17-1583269-C-T		not specified	Uncertain significance (Jan 26, 2022)
17-1583290-T-A		not specified	Uncertain significance (Nov 01, 2022)
17-1583316-T-C		not specified	Uncertain significance (Oct 20, 2023)
17-1583324-T-G		not specified	Uncertain significance (Oct 05, 2023)
17-1583330-C-G		not specified	Uncertain significance (Mar 08, 2024)
17-1583332-C-T		not specified	Uncertain significance (Sep 21, 2021)
17-1585920-C-T		not specified	Uncertain significance (Feb 15, 2023)
17-1585932-C-T		not specified	Uncertain significance (Apr 08, 2022)
17-1585946-G-T		not specified	Uncertain significance (Dec 15, 2023)
17-1586942-C-T			Benign (Dec 31, 2019)
17-1590850-C-T		not specified	Uncertain significance (Dec 27, 2023)
17-1590879-G-A		not specified	Uncertain significance (Feb 28, 2024)
17-1590897-A-T		not specified	Uncertain significance (Oct 12, 2021)
17-1591302-C-T		not specified	Uncertain significance (Jan 23, 2023)
17-1591328-C-T		not specified	Uncertain significance (Oct 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC43A2	protein_coding	protein_coding	ENST00000301335	13	59620

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00554	0.994	125717	0	22	125739	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.80	261	356	0.732	0.0000224	3665
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000182	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000932	0.0000924
European (Non-Finnish)	0.000126	0.000123
Middle Eastern	0.00	0.00
South Asian	0.0000660	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sodium-, chloride-, and pH-independent high affinity transport of large neutral amino acids. {ECO:0000269|PubMed:15659399}.
• Pathway: 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;Transport of small molecules;Methionine and cysteine metabolism;Valine, leucine and isoleucine degradation;Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.403
• rvis_EVS: -0.98
• rvis_percentile_EVS: 8.85

Haploinsufficiency Scores

• pHI: 0.317
• hipred: Y
• hipred_score: 0.610
• ghis: 0.558

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.210

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc43a2
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; liver/biliary system phenotype; immune system phenotype; digestive/alimentary phenotype

Gene ontology

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