SLC38A11

solute carrier family 38 member 11, the group of Solute carrier family 38

Basic information

Region (hg38): 2:164894354-164955525

Links

ENSG00000169507 ∙ NCBI:151258 ∙ OMIM:616526 ∙ HGNC:26836 ∙ Uniprot:Q08AI6 ∙ 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 SLC38A11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC38A11 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			32	1		33
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	32	1	1

Variants in SLC38A11

This is a list of pathogenic ClinVar variants found in the SLC38A11 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-164898463-T-G		not specified	Uncertain significance (Nov 18, 2022)
2-164898466-A-G		not specified	Uncertain significance (Mar 06, 2023)
2-164898471-T-G		not specified	Uncertain significance (Sep 13, 2023)
2-164898550-C-A		not specified	Uncertain significance (Aug 12, 2024)
2-164898610-C-A		not specified	Uncertain significance (Nov 21, 2023)
2-164898648-G-A		not specified	Uncertain significance (Apr 23, 2024)
2-164898699-A-G		not specified	Uncertain significance (Mar 01, 2024)
2-164898705-A-G		not specified	Uncertain significance (Jan 31, 2025)
2-164908659-C-T		not specified	Uncertain significance (Jan 17, 2024)
2-164908660-C-T		not specified	Uncertain significance (Feb 15, 2023)
2-164908689-G-A		not specified	Uncertain significance (Nov 15, 2024)
2-164908743-T-G		not specified	Uncertain significance (Jan 02, 2025)
2-164911638-C-G		not specified	Uncertain significance (Jul 05, 2024)
2-164911658-A-G		not specified	Uncertain significance (Jan 24, 2025)
2-164911659-T-C		not specified	Uncertain significance (Nov 12, 2024)
2-164911662-G-A		not specified	Uncertain significance (Jun 24, 2022)
2-164911670-A-C		not specified	Uncertain significance (Jun 09, 2022)
2-164911715-T-A		not specified	Uncertain significance (Mar 23, 2023)
2-164911739-A-G		not specified	Uncertain significance (Jun 13, 2024)
2-164915138-T-C		not specified	Uncertain significance (Jan 21, 2025)
2-164915148-T-C		not specified	Uncertain significance (Jul 13, 2021)
2-164915155-G-C		not specified	Likely benign (Dec 17, 2021)
2-164915159-A-G		not specified	Uncertain significance (Dec 26, 2023)
2-164915181-C-T		not specified	Uncertain significance (Aug 02, 2023)
2-164915202-G-A		not specified	Uncertain significance (Mar 05, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC38A11	protein_coding	protein_coding	ENST00000409149	10	59340

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.03e-15	0.00408	125656	0	89	125745	0.000354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0782	208	211	0.985	0.0000103	2642
Missense in Polyphen		71	73.137	0.97078		972
Synonymous	-0.334	80	76.3	1.05	0.00000400	812
Loss of Function	-0.697	20	16.9	1.18	7.96e-7	228

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000838	0.000834
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.000287	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000447	0.000440
Middle Eastern	0.000287	0.000272
South Asian	0.000253	0.000229
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative sodium-dependent amino acid/proton antiporter. {ECO:0000305}.

Intolerance Scores

• loftool: 0.793
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.45

Haploinsufficiency Scores

• pHI: 0.115
• hipred: N
• hipred_score: 0.197
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0890

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc38a11

Gene ontology

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