SLC39A10

solute carrier family 39 member 10, the group of Solute carrier family 39

Basic information

Region (hg38): 2:195575977-195737702

Links

ENSG00000196950 ∙ NCBI:57181 ∙ OMIM:608733 ∙ HGNC:20861 ∙ Uniprot:Q9ULF5 ∙ 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 SLC39A10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC39A10 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			42	2		44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	2	0

Variants in SLC39A10

This is a list of pathogenic ClinVar variants found in the SLC39A10 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-195680050-T-C		not specified	Uncertain significance (Apr 20, 2023)
2-195680069-T-A		not specified	Uncertain significance (Dec 28, 2023)
2-195680130-G-A		not specified	Uncertain significance (Jul 10, 2024)
2-195680163-C-T		not specified	Uncertain significance (Jan 23, 2025)
2-195680250-C-T		not specified	Uncertain significance (Dec 02, 2022)
2-195680349-G-T		not specified	Uncertain significance (Aug 23, 2021)
2-195680361-G-A		not specified	Uncertain significance (Feb 03, 2022)
2-195680368-T-C		not specified	Uncertain significance (Oct 03, 2023)
2-195680383-T-C		not specified	Uncertain significance (Jan 16, 2024)
2-195680502-G-A		not specified	Uncertain significance (Aug 07, 2024)
2-195680502-G-C		not specified	Uncertain significance (Jan 08, 2025)
2-195680517-A-G		not specified	Uncertain significance (Jun 19, 2024)
2-195680563-A-G		not specified	Uncertain significance (May 13, 2024)
2-195680572-G-A		not specified	Uncertain significance (Aug 13, 2021)
2-195680577-C-T		not specified	Likely benign (Feb 25, 2025)
2-195680578-G-A		not specified	Likely benign (May 14, 2024)
2-195680590-G-A		not specified	Uncertain significance (Jan 25, 2023)
2-195680706-G-A		not specified	Uncertain significance (Aug 02, 2021)
2-195680716-A-G		not specified	Uncertain significance (Mar 08, 2025)
2-195680728-C-A		not specified	Uncertain significance (Nov 15, 2021)
2-195680740-G-T		not specified	Uncertain significance (Jan 02, 2025)
2-195680814-G-C		not specified	Uncertain significance (Nov 20, 2024)
2-195680848-C-T		not specified	Uncertain significance (Jan 04, 2024)
2-195680885-T-A		not specified	Uncertain significance (Mar 03, 2025)
2-195680896-G-A		not specified	Likely benign (Feb 14, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC39A10	protein_coding	protein_coding	ENST00000409086	9	161726

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00730	125720	0	3	125723	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.95	334	451	0.741	0.0000224	5605
Missense in Polyphen		94	177.21	0.53045		2261
Synonymous	-0.0133	158	158	1.00	0.00000795	1508
Loss of Function	4.37	3	27.9	0.107	0.00000130	392

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000915	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a zinc-influx transporter. {ECO:0000269|PubMed:17359283}.
• Pathway: Nuclear Receptors Meta-Pathway;NRF2 pathway;Zinc homeostasis;Zinc influx into cells by the SLC39 gene family;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Metal ion SLC transporters;Zinc transporters (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.139
• rvis_EVS: -0.16
• rvis_percentile_EVS: 42.16

Haploinsufficiency Scores

• pHI: 0.855
• hipred: Y
• hipred_score: 0.654
• ghis: 0.572

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.182

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc39a10
• 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); endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; 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); hematopoietic system phenotype; immune system phenotype

Zebrafish Information Network

• Gene name: slc39a10
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: bent

Gene ontology

• Biological process: negative regulation of B cell apoptotic process;cellular zinc ion homeostasis;positive regulation of B cell proliferation;positive regulation of B cell receptor signaling pathway;zinc ion import across plasma membrane;positive regulation of protein tyrosine phosphatase activity
• Cellular component: integral component of plasma membrane
• Molecular function: zinc ion transmembrane transporter activity