SLC7A10

solute carrier family 7 member 10, the group of Solute carrier family 7

Basic information

Region (hg38): 19:33208664-33225850

Links

ENSG00000130876 ∙ NCBI:56301 ∙ OMIM:607959 ∙ HGNC:11058 ∙ Uniprot:Q9NS82 ∙ 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 SLC7A10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC7A10 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			32	10	1	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					10	10
Total	0	0	32	10	13

Variants in SLC7A10

This is a list of pathogenic ClinVar variants found in the SLC7A10 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-33208703-G-A			Benign (May 17, 2021)
19-33208758-T-TA			Benign (May 15, 2021)
19-33208899-G-A		not specified	Uncertain significance (Aug 19, 2024)
19-33208956-C-T		not specified	Uncertain significance (May 29, 2024)
19-33208962-C-G		not specified	Uncertain significance (Apr 29, 2024)
19-33208962-C-T		not specified	Uncertain significance (Oct 17, 2024)
19-33208968-C-A		not specified	Likely benign (Dec 12, 2023)
19-33208986-C-T		not specified	Uncertain significance (Aug 26, 2024)
19-33209009-T-C		not specified	Likely benign (Jun 21, 2023)
19-33209016-T-C		not specified	Uncertain significance (Jan 31, 2024)
19-33209172-C-T			Benign (May 16, 2021)
19-33209316-C-T		not specified	Uncertain significance (Aug 20, 2023)
19-33209337-C-T		not specified	Uncertain significance (Jul 21, 2022)
19-33209352-C-T		not specified	Uncertain significance (Feb 16, 2023)
19-33209360-G-C		not specified	Uncertain significance (Jun 13, 2023)
19-33209375-C-A			Benign (May 04, 2021)
19-33209392-C-T		not specified	Likely benign (Dec 06, 2021)
19-33209539-C-T			Benign (May 15, 2021)
19-33210486-G-A		not specified	Uncertain significance (Jun 29, 2022)
19-33210492-C-T			Benign (May 06, 2021)
19-33210493-G-A		not specified	Uncertain significance (Sep 06, 2022)
19-33210501-C-T		not specified	Uncertain significance (Apr 24, 2024)
19-33210529-C-T		not specified	Uncertain significance (Nov 13, 2024)
19-33210589-C-T		not specified	Uncertain significance (May 13, 2024)
19-33210598-T-C		not specified	Uncertain significance (Dec 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC7A10	protein_coding	protein_coding	ENST00000253188	11	17187

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000139	0.992	125701	0	42	125743	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.11	265	321	0.826	0.0000199	3312
Missense in Polyphen		113	135.23	0.83562		1429
Synonymous	0.266	148	152	0.973	0.0000112	1124
Loss of Function	2.36	10	21.9	0.456	0.00000103	237

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000198	0.000185
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000136	0.000132
Middle Eastern	0.00	0.00
South Asian	0.000674	0.000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sodium-independent, high affinity transport of small neutral D- and L-amino acids. May play a role in the modulation of glutamatergic transmission through mobilization of D-serine at the glutamatergic synapse. {ECO:0000269|PubMed:10863037}.
• Pathway: Differentiation of white and brown adipocyte;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;Aminosugars metabolism;Glycerophospholipid metabolism;Cell surface interactions at the vascular wall;Hemostasis;Basigin interactions;Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.181
• rvis_EVS: -0.57
• rvis_percentile_EVS: 18.9

Haploinsufficiency Scores

• pHI: 0.106
• hipred: N
• hipred_score: 0.456
• ghis: 0.444

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.146

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc7a10
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; muscle phenotype; growth/size/body region phenotype

Gene ontology

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