SLC39A9

solute carrier family 39 member 9, the group of Solute carrier family 39

Basic information

Region (hg38): 14:69398015-69462390

Links

ENSG00000029364 ∙ NCBI:55334 ∙ OMIM:619116 ∙ HGNC:20182 ∙ Uniprot:Q9NUM3 ∙ 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 SLC39A9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC39A9 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	1

Variants in SLC39A9

This is a list of pathogenic ClinVar variants found in the SLC39A9 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-69424104-A-G		not specified	Uncertain significance (Apr 19, 2024)
14-69442159-A-G		not specified	Uncertain significance (Dec 16, 2023)
14-69442200-G-A		not specified	Uncertain significance (Dec 21, 2024)
14-69442234-A-G		not specified	Uncertain significance (Jan 18, 2025)
14-69442249-A-G		not specified	Uncertain significance (Apr 08, 2024)
14-69458404-G-A			Benign (Jun 18, 2018)
14-69458423-G-A		not specified	Uncertain significance (Oct 07, 2024)
14-69458492-C-T		not specified	Uncertain significance (Jun 25, 2024)
14-69458495-G-A		not specified	Uncertain significance (Oct 30, 2023)
14-69458502-C-T		not specified	Uncertain significance (Dec 25, 2024)
14-69458522-C-T		not specified	Uncertain significance (Dec 04, 2024)
14-69458523-G-A		not specified	Uncertain significance (Apr 12, 2022)
14-69458523-G-T		not specified	Uncertain significance (May 20, 2024)
14-69458560-C-G		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC39A9	protein_coding	protein_coding	ENST00000336643	7	64374

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.729	0.270	125741	0	5	125746	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.97	103	177	0.582	0.00000923	1966
Missense in Polyphen		34	69.764	0.48736		790
Synonymous	0.710	65	72.7	0.894	0.00000419	676
Loss of Function	2.83	2	13.0	0.154	7.12e-7	153

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a zinc-influx transporter. {ECO:0000250}.
• Pathway: Nuclear Receptors Meta-Pathway;NRF2 pathway;Zinc homeostasis (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.478
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.82

Haploinsufficiency Scores

• pHI: 0.716
• hipred: Y
• hipred_score: 0.673
• ghis: 0.567

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.589

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc39a9

Gene ontology

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