SLC39A12

solute carrier family 39 member 12, the group of Solute carrier family 39

Basic information

Region (hg38): 10:17951838-18043292

Links

ENSG00000148482 ∙ NCBI:221074 ∙ OMIM:608734 ∙ HGNC:20860 ∙ Uniprot:Q504Y0 ∙ 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 SLC39A12 gene.

• Inborn genetic diseases (22 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC39A12 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		1
missense			20	2	1	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	20	3	1

Variants in SLC39A12

This is a list of pathogenic ClinVar variants found in the SLC39A12 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-17953286-C-T		not specified	Likely benign (Oct 03, 2022)
10-17953322-C-G		not specified	Uncertain significance (Jan 02, 2024)
10-17953404-C-T		not specified	Likely benign (Jan 04, 2022)
10-17953415-C-A		not specified	Uncertain significance (Apr 08, 2022)
10-17953442-C-T		not specified	Uncertain significance (Jan 04, 2022)
10-17953471-C-G		not specified	Uncertain significance (Dec 06, 2021)
10-17953533-A-G		not specified	Uncertain significance (May 25, 2022)
10-17961572-CT-C			Benign (Dec 31, 2019)
10-17961683-A-G		not specified	Uncertain significance (Feb 15, 2023)
10-17961692-C-G		not specified	Uncertain significance (Mar 14, 2023)
10-17961698-G-C		not specified	Uncertain significance (Jan 23, 2024)
10-17961713-A-G		not specified	Uncertain significance (Aug 14, 2023)
10-17965508-A-G		not specified	Uncertain significance (Feb 16, 2023)
10-17965548-T-A		not specified	Uncertain significance (Jan 04, 2024)
10-17965610-A-C		not specified	Uncertain significance (Aug 03, 2022)
10-17965636-T-C		not specified	Uncertain significance (Aug 17, 2022)
10-17965658-C-T		not specified	Likely benign (Nov 09, 2023)
10-17977913-C-G		not specified	Uncertain significance (Apr 25, 2023)
10-17978031-C-T		not specified	Uncertain significance (Oct 29, 2021)
10-17981381-G-A			Benign (Dec 31, 2019)
10-17981405-A-G		not specified	Uncertain significance (Dec 20, 2023)
10-17987479-A-C		not specified	Uncertain significance (Jul 14, 2023)
10-17987490-A-G		not specified	Uncertain significance (Apr 08, 2022)
10-17987523-T-C		not specified	Uncertain significance (Apr 24, 2023)
10-17987607-G-A		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC39A12	protein_coding	protein_coding	ENST00000377369	12	91454

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.34e-7	0.996	125705	0	43	125748	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.285	375	360	1.04	0.0000177	4522
Missense in Polyphen		103	117.13	0.87936		1517
Synonymous	-0.393	145	139	1.04	0.00000719	1346
Loss of Function	2.57	15	30.3	0.495	0.00000135	390

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000307	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.000761	0.000761
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000761	0.000761
South Asian	0.000262	0.000261
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a zinc-influx transporter (Potential). May be partly involved in the outbreak of schizophrenia. {ECO:0000305}.
• Pathway: Nuclear Receptors Meta-Pathway;NRF2 pathway;Zinc homeostasis (Consensus)

Recessive Scores

• pRec: 0.0921

Intolerance Scores

• loftool: 0.865
• rvis_EVS: 0.71
• rvis_percentile_EVS: 85.82

Haploinsufficiency Scores

• pHI: 0.266
• hipred: N
• hipred_score: 0.324
• ghis: 0.465

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.164

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc39a12

Gene ontology

• Biological process: cellular zinc ion homeostasis;signal transduction;regulation of neuron projection development;regulation of microtubule polymerization;zinc ion import across plasma membrane
• Cellular component: integral component of plasma membrane;perinuclear region of cytoplasm;extracellular vesicle
• Molecular function: zinc ion transmembrane transporter activity