SLC38A10

solute carrier family 38 member 10, the group of Solute carrier family 38

Basic information

Region (hg38): 17:81244811-81295547

Links

ENSG00000157637

∙ NCBI:124565 ∙ OMIM:616525 ∙ HGNC:28237 ∙ Uniprot:Q9HBR0 ∙ 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 SLC38A10 gene.

not_specified (117 variants)
SLC38A10-related_disorder (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC38A10 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001037984.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar	1 clinvar	4
missense			104 clinvar	14 clinvar		118
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	104	17	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC38A10	protein_coding	protein_coding	ENST00000374759	16	50548

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.43e-10	0.970	125647	0	100	125747	0.000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.566	679	722	0.941	0.0000475	7176
Missense in Polyphen		195	232.86	0.83741		2380
Synonymous	-0.373	331	322	1.03	0.0000238	2381
Loss of Function	2.20	21	35.0	0.599	0.00000175	385

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000465	0.000420
Ashkenazi Jewish	0.00124	0.00119
East Asian	0.000505	0.000489
Finnish	0.000147	0.000139
European (Non-Finnish)	0.000472	0.000448
Middle Eastern	0.000505	0.000489
South Asian	0.000462	0.000425
Other	0.000349	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Putative sodium-dependent amino acid/proton antiporter. {ECO:0000250}.;

Recessive Scores

pRec: 0.0945

Intolerance Scores

loftool: 0.802
rvis_EVS: 1.13
rvis_percentile_EVS: 92.24

Haploinsufficiency Scores

pHI: 0.114
hipred: N
hipred_score: 0.306
ghis: 0.559

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.487

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

Gene name: Slc38a10
Phenotype: immune system phenotype; skeleton phenotype; vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; craniofacial phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan);

Gene ontology

Biological process: amino acid transmembrane transport;sodium ion transport;bone development
Cellular component: Golgi apparatus;integral component of membrane
Molecular function: amino acid transmembrane transporter activity