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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 55.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_020342.3	NP_065075.1	9	yes	-
ENST00000359634.10	ENSP00000352655.5	9	yes	-
NM_001127257.2	NP_001120729.1	9	-	-
ENST00000409086.7	ENSP00000386766.3	9	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC39A10 gene.

• not_specified (83 variants)

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. These statistics are base on transcript: NM_020342.3. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1			1
missense			75	9		84
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3			3
Total	0	0	79	9	0

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
		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

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

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