SLC39A11

solute carrier family 39 member 11, the group of Solute carrier family 39

Basic information

Region (hg38): 17:72645948-73092712

Previous symbols: [ "C17orf26" ]

Links

ENSG00000133195 ∙ NCBI:201266 ∙ OMIM:616508 ∙ HGNC:14463 ∙ Uniprot:Q8N1S5 ∙ 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 SLC39A11 gene.

• Inborn genetic diseases (17 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC39A11 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				2	1	3
missense			16	2	1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	4	2

Variants in SLC39A11

This is a list of pathogenic ClinVar variants found in the SLC39A11 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-72647598-C-T		not specified	Uncertain significance (Jun 16, 2023)
17-72648840-C-T		not specified	Uncertain significance (Apr 25, 2022)
17-72649213-G-T		not specified	Uncertain significance (Aug 02, 2021)
17-72736677-G-A		not specified	Uncertain significance (Jan 17, 2024)
17-72849640-C-A		Ependymoma	Uncertain significance (Dec 29, 2017)
17-72849643-T-C		not specified	Uncertain significance (May 27, 2022)
17-72849651-G-A		not specified	Uncertain significance (Dec 31, 2023)
17-72849678-C-T		not specified	Uncertain significance (Jul 13, 2021)
17-72849683-C-G		not specified	Uncertain significance (Jun 09, 2022)
17-72849693-C-T		not specified	Uncertain significance (Nov 06, 2023)
17-72849738-G-A		not specified	Uncertain significance (Feb 21, 2024)
17-72849742-C-T		not specified	Uncertain significance (Dec 13, 2022)
17-72947746-C-T		not specified	Uncertain significance (Nov 28, 2023)
17-72947776-C-T		not specified	Uncertain significance (Nov 07, 2022)
17-72947793-G-A		not specified	Uncertain significance (Dec 27, 2023)
17-72947834-G-A			Likely benign (Sep 01, 2022)
17-72947869-C-T			Likely benign (Dec 27, 2017)
17-73031561-G-C		not specified	Uncertain significance (May 31, 2023)
17-73031573-G-A		not specified	Uncertain significance (May 16, 2023)
17-73031602-A-G		not specified	Uncertain significance (Apr 20, 2023)
17-73031606-T-C		not specified	Uncertain significance (Sep 27, 2021)
17-73031625-G-C		not specified	Uncertain significance (Aug 02, 2021)
17-73031663-C-A		not specified	Uncertain significance (Sep 26, 2023)
17-73031709-C-T		not specified	Uncertain significance (Mar 01, 2023)
17-73084833-T-C		not specified	Uncertain significance (Jan 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC39A11	protein_coding	protein_coding	ENST00000542342	9	446764

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.35e-18	0.000286	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.127	206	201	1.03	0.0000112	2178
Missense in Polyphen		94	95.626	0.983		1011
Synonymous	-0.405	91	86.2	1.06	0.00000584	740
Loss of Function	-1.55	23	16.3	1.42	8.39e-7	172

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000338	0.000334
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000212	0.000211
Middle Eastern	0.000110	0.000109
South Asian	0.000131	0.000131
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a cellular zinc transporter. {ECO:0000250|UniProtKB:Q8BWY7}.
• Pathway: Nuclear Receptors Meta-Pathway;NRF2 pathway;Zinc homeostasis (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.860
• rvis_EVS: 0.64
• rvis_percentile_EVS: 84.05

Haploinsufficiency Scores

• pHI: 0.190
• hipred: N
• hipred_score: 0.289
• ghis: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0935

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc39a11

Gene ontology

• Biological process: zinc ion transmembrane transport
• Cellular component: fungal-type vacuole membrane;nucleus;cytoplasm;Golgi apparatus;plasma membrane;integral component of membrane
• Molecular function: zinc ion transmembrane transporter activity