SLC39A3

solute carrier family 39 member 3, the group of Solute carrier family 39

Basic information

Region (hg38): 19:2732204-2740028

Links

ENSG00000141873 ∙ NCBI:29985 ∙ OMIM:612168 ∙ HGNC:17128 ∙ Uniprot:Q9BRY0 ∙ 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 SLC39A3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC39A3 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			33		1	34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	0	1

Variants in SLC39A3

This is a list of pathogenic ClinVar variants found in the SLC39A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-2732774-C-T		not specified	Uncertain significance (Jul 13, 2022)
19-2732782-A-G		not specified	Uncertain significance (Apr 13, 2023)
19-2732833-T-C		not specified	Uncertain significance (Jul 27, 2024)
19-2732885-C-T		not specified	Uncertain significance (Jun 17, 2022)
19-2732890-G-A		not specified	Uncertain significance (Jun 02, 2023)
19-2732909-C-T		not specified	Uncertain significance (Jan 17, 2023)
19-2732926-G-A		not specified	Uncertain significance (Aug 16, 2022)
19-2732939-C-T		not specified	Uncertain significance (Mar 15, 2024)
19-2732940-G-C		not specified	Uncertain significance (Nov 10, 2022)
19-2732941-C-T		not specified	Uncertain significance (May 17, 2023)
19-2732984-C-T		not specified	Uncertain significance (Oct 07, 2024)
19-2732990-C-T		not specified	Uncertain significance (Sep 01, 2021)
19-2733010-G-A		not specified	Uncertain significance (Aug 10, 2024)
19-2733012-G-C		not specified	Uncertain significance (Oct 16, 2023)
19-2733016-C-T		not specified	Uncertain significance (Oct 21, 2024)
19-2733017-G-A		not specified	Uncertain significance (Sep 16, 2021)
19-2733023-G-A		not specified	Uncertain significance (May 17, 2023)
19-2733023-G-T		not specified	Uncertain significance (Jul 19, 2023)
19-2733024-C-T		not specified	Uncertain significance (Nov 04, 2022)
19-2733059-C-T		not specified	Uncertain significance (Oct 20, 2023)
19-2733080-C-T		not specified	Likely benign (Nov 10, 2024)
19-2733163-G-A		not specified	Uncertain significance (Oct 26, 2022)
19-2733169-G-A		not specified	Uncertain significance (Feb 12, 2024)
19-2733190-C-T			Benign (Oct 10, 2018)
19-2733191-G-A		not specified	Uncertain significance (Apr 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC39A3	protein_coding	protein_coding	ENST00000269740	2	7949

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.120	0.788	125709	0	11	125720	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.669	189	217	0.872	0.0000154	2005
Missense in Polyphen		60	73.328	0.81824		714
Synonymous	-2.40	152	119	1.28	0.00000999	719
Loss of Function	1.34	2	5.33	0.375	2.25e-7	70

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.000109	0.000109
South Asian	0.0000664	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a zinc-influx transporter. {ECO:0000305}.
• 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: 0.117

Intolerance Scores

• loftool: 0.104
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.09

Haploinsufficiency Scores

• pHI: 0.216
• hipred: N
• hipred_score: 0.459
• ghis: 0.510

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.497

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc39a3
• Phenotype: embryo phenotype; hematopoietic system phenotype; limbs/digits/tail phenotype; immune system 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; craniofacial phenotype

Gene ontology

• Biological process: cell morphogenesis;in utero embryonic development;T cell homeostasis;embryonic cranial skeleton morphogenesis;limb development;zinc ion transmembrane transport
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: zinc ion transmembrane transporter activity