SLC39A2

solute carrier family 39 member 2, the group of Solute carrier family 39

Basic information

Region (hg38): 14:20999255-21001871

Links

ENSG00000165794 ∙ NCBI:29986 ∙ OMIM:612166 ∙ HGNC:17127 ∙ Uniprot:Q9NP94 ∙ 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 SLC39A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC39A2 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			14	1	2	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	3

Variants in SLC39A2

This is a list of pathogenic ClinVar variants found in the SLC39A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-20999501-A-C		not specified	Uncertain significance (Apr 29, 2024)
14-20999510-T-C		not specified	Uncertain significance (Jun 24, 2022)
14-20999540-T-C		not specified	Uncertain significance (May 28, 2024)
14-20999754-T-G			Benign (Feb 25, 2021)
14-20999816-A-G		not specified	Uncertain significance (Jan 17, 2024)
14-20999827-A-C		not specified	Uncertain significance (Dec 20, 2023)
14-21000121-A-T		not specified	Uncertain significance (Dec 19, 2022)
14-21000165-A-T		not specified	Uncertain significance (May 13, 2024)
14-21001079-G-A		not specified	Uncertain significance (Dec 13, 2022)
14-21001082-C-T			Benign (Jun 05, 2018)
14-21001111-T-A		not specified	Uncertain significance (Jun 28, 2022)
14-21001130-G-T		not specified	Uncertain significance (Sep 16, 2021)
14-21001209-C-T		not specified	Uncertain significance (Apr 07, 2022)
14-21001210-G-A			Benign (Jun 05, 2018)
14-21001223-A-G		not specified	Uncertain significance (Oct 05, 2023)
14-21001287-G-A		not specified	Uncertain significance (Nov 10, 2022)
14-21001351-G-A		not specified	Uncertain significance (Sep 29, 2023)
14-21001356-C-G		not specified	Uncertain significance (Oct 25, 2023)
14-21001373-G-C		not specified	Uncertain significance (Feb 10, 2022)
14-21001410-G-A		not specified	Likely benign (Jul 06, 2021)
14-21001538-G-A		not specified	Uncertain significance (Dec 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC39A2	protein_coding	protein_coding	ENST00000298681	4	2617

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000720	0.758	125390	1	354	125745	0.00141

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.467	185	168	1.10	0.00000853	1934
Missense in Polyphen		76	67.552	1.1251		850
Synonymous	0.566	64	70.0	0.914	0.00000359	698
Loss of Function	1.08	8	12.1	0.663	6.69e-7	139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00233	0.00233
Ashkenazi Jewish	0.0109	0.0109
East Asian	0.00158	0.00158
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000510	0.000510
Middle Eastern	0.00158	0.00158
South Asian	0.00219	0.00216
Other	0.00261	0.00261

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates zinc uptake. Zinc uptake may be mediated by a Zn(2+)-HCO(3)(-) symport mechanism and can function in the presence of albumin. May also transport other divalent cations. May be important in contact inhibition of normal epithelial cells and loss of its expression may play a role in tumorigenesis.
• Pathway: Nuclear Receptors Meta-Pathway;NRF2 pathway;Zinc homeostasis;Senescence and Autophagy in Cancer;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: 0.0927

Intolerance Scores

• loftool: 0.786
• rvis_EVS: 1.82
• rvis_percentile_EVS: 96.97

Haploinsufficiency Scores

• pHI: 0.104
• hipred: N
• hipred_score: 0.144

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.124

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc39a2
• Phenotype: homeostasis/metabolism phenotype; craniofacial 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); growth/size/body region phenotype; liver/biliary system phenotype; limbs/digits/tail phenotype; embryo phenotype

Gene ontology

• Biological process: zinc ion transport;zinc ion transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;cytoplasmic vesicle
• Molecular function: zinc ion transmembrane transporter activity