SLC38A5

solute carrier family 38 member 5, the group of Solute carrier family 38

Basic information

Region (hg38): X:48458537-48470260

Links

ENSG00000017483 ∙ NCBI:92745 ∙ OMIM:300649 ∙ HGNC:18070 ∙ Uniprot:Q8WUX1 ∙ 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 SLC38A5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC38A5 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				2		2
missense			14	3	1	18
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	14	6	1

Variants in SLC38A5

This is a list of pathogenic ClinVar variants found in the SLC38A5 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-48458699-TTCC-T			Likely benign (Mar 01, 2023)
X-48458949-C-T		not specified	Likely benign (Dec 27, 2023)
X-48459000-A-G		not specified	Benign (Mar 29, 2016)
X-48459019-C-T		not specified	Uncertain significance (Aug 10, 2021)
X-48459542-C-T			Likely benign (Feb 01, 2023)
X-48459752-C-T		not specified	Likely benign (Jun 26, 2023)
X-48460752-G-A		not specified	Uncertain significance (Jun 14, 2022)
X-48461052-C-T		not specified	Uncertain significance (Sep 27, 2021)
X-48461076-G-A		not specified	Uncertain significance (Nov 17, 2022)
X-48461719-G-A		not specified	Uncertain significance (Oct 06, 2024)
X-48461763-A-G		Abnormality of neuronal migration	Uncertain significance (Oct 31, 2014)
X-48462054-C-T		not specified	Uncertain significance (Apr 01, 2024)
X-48462074-A-G		not specified	Likely benign (Feb 25, 2025)
X-48462268-G-A		not specified	Uncertain significance (Sep 23, 2023)
X-48462947-G-T			Likely benign (Mar 01, 2023)
X-48462952-T-G		not specified	Uncertain significance (Apr 19, 2023)
X-48466236-C-T			Uncertain significance (Dec 02, 2023)
X-48466292-C-T		not specified	Uncertain significance (Jan 02, 2025)
X-48466313-G-A		not specified	Uncertain significance (Aug 30, 2021)
X-48466838-A-G		not specified	Uncertain significance (May 26, 2023)
X-48467726-G-A		SLC38A5-related disorder	Likely benign (Jun 08, 2023)
X-48467750-C-T		not specified	Likely benign (Oct 07, 2024)
X-48467751-G-C		not specified	Uncertain significance (Apr 15, 2024)
X-48467771-C-A		not specified	Uncertain significance (Nov 10, 2024)
X-48467771-C-T		not specified	Likely benign (Dec 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC38A5	protein_coding	protein_coding	ENST00000376876	15	11725

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.977	0.0232	124370	1	0	124371	0.00000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.44	91	184	0.494	0.0000147	3054
Missense in Polyphen		21	62.617	0.33537		1177
Synonymous	0.295	73	76.3	0.957	0.00000651	962
Loss of Function	3.47	1	16.0	0.0627	0.00000116	286

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000123	0.00000889
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a sodium-dependent amino acid transporter which countertransport protons. Mediates the saturable, pH- sensitive, and electrogenic cotransport of several neutral amino acids including glycine, asparagine, alanine, serine, glutamine and histidine with sodium. {ECO:0000269|PubMed:11243884}.
• Pathway: GABAergic synapse - Homo sapiens (human);Glutaminolysis and Cancer;miR-targeted genes in muscle cell - TarBase;Amino acid transport across the plasma membrane;Amino acid and oligopeptide SLC transporters;Fibroblast growth factor-1;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Histidine metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Aminosugars metabolism;Glycerophospholipid metabolism;Porphyrin metabolism;Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

• pRec: 0.242

Intolerance Scores

• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.0758
• hipred: Y
• hipred_score: 0.707
• ghis: 0.408

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.266

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc38a5
• Phenotype: homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: amino acid transmembrane transport;amino acid transport;glycine transport
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: amino acid transmembrane transporter activity;glycine transmembrane transporter activity