SLC38A10

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

Basic information

Region (hg38): 17:81244811-81295547

Links

ENSG00000157637NCBI:124565OMIM:616525HGNC:28237Uniprot:Q9HBR0AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC38A10 gene.

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.

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
1
clinvar
1
clinvar
2
missense
55
clinvar
11
clinvar
66
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 55 12 1

Variants in SLC38A10

This is a list of pathogenic ClinVar variants found in the SLC38A10 region.

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

Position Type Phenotype Significance ClinVar
17-81245603-G-A not specified Uncertain significance (Aug 10, 2021)2242389
17-81245636-G-A not specified Uncertain significance (Oct 26, 2021)2357189
17-81245851-A-G SLC38A10-related disorder Likely benign (Apr 28, 2022)3034657
17-81245997-C-G not specified Uncertain significance (Jul 13, 2021)3164547
17-81246100-G-A not specified Likely benign (Jul 13, 2021)2368127
17-81246137-T-C SLC38A10-related disorder Likely benign (May 22, 2020)3037674
17-81246203-T-C not specified Likely benign (Jul 26, 2021)2239374
17-81246221-C-A SLC38A10-related disorder Uncertain significance (Sep 11, 2024)3355717
17-81246298-C-T not specified Likely benign (Sep 01, 2021)2248189
17-81246326-C-T not specified Uncertain significance (Sep 01, 2021)2220356
17-81251240-C-T SLC38A10-related disorder Likely benign (Aug 12, 2022)3050225
17-81251439-G-A SLC38A10-related disorder Likely benign (May 30, 2023)3041712
17-81251510-G-A not specified Uncertain significance (May 15, 2023)2546355
17-81251525-G-A not specified Likely benign (Dec 14, 2023)3164545
17-81251528-C-T not specified Uncertain significance (Dec 03, 2021)2379290
17-81251548-G-A SLC38A10-related disorder Likely benign (Sep 25, 2020)3031872
17-81251564-A-C not specified Uncertain significance (Jan 04, 2022)2269136
17-81251573-C-A not specified Uncertain significance (Jul 14, 2023)2611968
17-81252216-G-T not specified Uncertain significance (Nov 07, 2024)3444300
17-81252242-C-A not specified Uncertain significance (Aug 02, 2021)2246670
17-81252248-G-A not specified Likely benign (Apr 25, 2022)2379787
17-81252251-G-A not specified Uncertain significance (Feb 28, 2023)2469994
17-81252258-C-T not specified Uncertain significance (Feb 10, 2022)2356690
17-81252291-C-T not specified Uncertain significance (Jan 29, 2024)3164544
17-81252330-G-A not specified Uncertain significance (Feb 16, 2023)2463917

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SLC38A10protein_codingprotein_codingENST00000374759 1650548
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.43e-100.97012564701001257470.000398
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.5666797220.9410.00004757176
Missense in Polyphen195232.860.837412380
Synonymous-0.3733313221.030.00002382381
Loss of Function2.202135.00.5990.00000175385

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004650.000420
Ashkenazi Jewish0.001240.00119
East Asian0.0005050.000489
Finnish0.0001470.000139
European (Non-Finnish)0.0004720.000448
Middle Eastern0.0005050.000489
South Asian0.0004620.000425
Other0.0003490.000326

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

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh

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