SLC39A1

solute carrier family 39 member 1, the group of MicroRNA protein coding host genes|Solute carrier family 39

Basic information

Region (hg38): 1:153959099-153968184

Previous symbols: [ "ZIRTL" ]

Links

ENSG00000143570 ∙ NCBI:27173 ∙ OMIM:604740 ∙ HGNC:12876 ∙ Uniprot:Q9NY26 ∙ 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 SLC39A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC39A1 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in SLC39A1

This is a list of pathogenic ClinVar variants found in the SLC39A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-153960159-T-C		not specified	Uncertain significance (Nov 20, 2024)
1-153960163-G-A		not specified	Uncertain significance (May 06, 2022)
1-153960180-C-G		not specified	Likely benign (Aug 10, 2021)
1-153960180-C-T		not specified	Uncertain significance (Aug 21, 2024)
1-153960181-T-G		not specified	Uncertain significance (Dec 09, 2024)
1-153960217-T-G		not specified	Uncertain significance (Apr 12, 2023)
1-153960243-C-G		not specified	Uncertain significance (May 21, 2024)
1-153960280-C-T		not specified	Uncertain significance (Nov 07, 2023)
1-153960322-G-A		not specified	Uncertain significance (Jan 31, 2023)
1-153960358-C-A		not specified	Uncertain significance (Jan 05, 2022)
1-153960390-C-T		not specified	Uncertain significance (Aug 28, 2024)
1-153960439-G-T		not specified	Uncertain significance (Oct 13, 2023)
1-153960457-G-A		not specified	Uncertain significance (Jun 28, 2023)
1-153960468-C-T		not specified	Uncertain significance (Apr 15, 2024)
1-153960489-C-T		not specified	Uncertain significance (Feb 16, 2023)
1-153960532-A-G		not specified	Uncertain significance (Oct 26, 2022)
1-153960541-A-T		not specified	Uncertain significance (Oct 05, 2023)
1-153960606-G-A		not specified	Uncertain significance (Feb 08, 2023)
1-153962221-G-A		not specified	Uncertain significance (Aug 14, 2024)
1-153962541-G-A		not specified	Uncertain significance (Jun 29, 2023)
1-153962546-G-T		not specified	Uncertain significance (Sep 25, 2023)
1-153962585-C-T		not specified	Uncertain significance (Sep 22, 2022)
1-153962631-C-T		not specified	Uncertain significance (Sep 09, 2024)
1-153962633-T-C		not specified	Uncertain significance (Jan 26, 2022)
1-153962697-G-A		not specified	Uncertain significance (Feb 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC39A1	protein_coding	protein_coding	ENST00000368623	3	8614

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.126	0.853	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.953	145	181	0.801	0.00000966	2002
Missense in Polyphen		30	46.132	0.65031		581
Synonymous	1.21	73	87.4	0.835	0.00000464	791
Loss of Function	1.99	3	9.66	0.310	4.95e-7	107

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000294	0.000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates zinc uptake. May function as a major endogenous zinc uptake transporter in many cells of the body. Responsible for the rapid uptake and accumulation of physiologically effective zinc in prostate cells. {ECO:0000269|PubMed:12888280}.
• 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: 0.231

Intolerance Scores

• loftool: 0.579
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.75

Haploinsufficiency Scores

• pHI: 0.491
• hipred: N
• hipred_score: 0.242
• ghis: 0.579

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.536

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc39a1
• Phenotype: limbs/digits/tail phenotype; embryo phenotype; normal phenotype; craniofacial phenotype; growth/size/body region 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)

Gene ontology

• Biological process: in utero embryonic development;cation transport;embryonic cranial skeleton morphogenesis;limb development;zinc ion transmembrane transport
• Cellular component: endoplasmic reticulum membrane;plasma membrane;membrane;integral component of membrane
• Molecular function: signaling receptor binding;zinc ion transmembrane transporter activity;inorganic cation transmembrane transporter activity