SLC39A13

solute carrier family 39 member 13, the group of Solute carrier family 39

Basic information

Region (hg38): 11:47407132-47416496

Links

ENSG00000165915 ∙ NCBI:91252 ∙ OMIM:608735 ∙ HGNC:20859 ∙ Uniprot:Q96H72 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spondyloepimetaphyseal dysplasia-abnormal dentition syndrome (Definitive), mode of inheritance: AR
• Ehlers-Danlos syndrome, spondylocheirodysplastic type (Definitive), mode of inheritance: AR
• Ehlers-Danlos syndrome, spondylocheirodysplastic type (Strong), mode of inheritance: AR
• Ehlers-Danlos syndrome, spondylocheirodysplastic type (Strong), mode of inheritance: AR
• Ehlers-Danlos syndrome, spondylocheirodysplastic type (Strong), mode of inheritance: AR
• Ehlers-Danlos syndrome, spondylocheirodysplastic type (Supportive), mode of inheritance: AR
• Ehlers-Danlos syndrome, spondylocheirodysplastic type (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ehlers-Danlos syndrome, spondylodysplastic type, 3	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Dermatologic; Musculoskeletal	18985159; 18513683

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC39A13 gene.

• Ehlers-Danlos syndrome, spondylocheirodysplastic type (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC39A13 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			4	89	1	94
missense			88	3	3	94
nonsense		1	2			3
start loss						0
frameshift			2			2
inframe indel	1		3			4
splice donor/acceptor (+/-2bp)			1			1
splice region			8	15	1	24
non coding			2	53	15	70
Total	1	1	102	145	19

Variants in SLC39A13

This is a list of pathogenic ClinVar variants found in the SLC39A13 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-47408638-G-C		not specified	Likely benign (Oct 23, 2017)
11-47408639-G-T		not specified	Likely benign (Mar 09, 2018)
11-47408641-T-TCGC			Benign (May 30, 2018)
11-47408665-G-A		Ehlers-Danlos syndrome	Uncertain significance (Dec 11, 2020)
11-47408665-G-T			Uncertain significance (May 30, 2017)
11-47408907-T-C			Benign (Jun 23, 2018)
11-47408918-T-C		Ehlers-Danlos syndrome, spondylocheirodysplastic type	Uncertain significance (Jan 22, 2021)
11-47409739-T-G			Benign (Aug 07, 2018)
11-47409752-A-G			Likely benign (Jul 14, 2018)
11-47409959-C-T			Likely benign (Jul 14, 2018)
11-47409978-G-A			Benign (Jun 26, 2018)
11-47410014-G-A			Benign (Aug 12, 2018)
11-47410069-G-T		not specified	Likely benign (Nov 28, 2017)
11-47410071-C-A		not specified	Likely benign (Nov 13, 2017)
11-47410116-G-A		Inborn genetic diseases	Uncertain significance (Mar 15, 2024)
11-47410117-G-T		Ehlers-Danlos syndrome, spondylocheirodysplastic type • Inborn genetic diseases	Uncertain significance (May 03, 2023)
11-47410125-A-G		Ehlers-Danlos syndrome, spondylocheirodysplastic type • Inborn genetic diseases	Uncertain significance (Feb 23, 2023)
11-47410126-T-C		Inborn genetic diseases	Uncertain significance (Feb 07, 2023)
11-47410129-C-T		Ehlers-Danlos syndrome, spondylocheirodysplastic type	Uncertain significance (Aug 04, 2023)
11-47410130-G-A		Ehlers-Danlos syndrome, spondylocheirodysplastic type	Likely benign (Feb 23, 2023)
11-47410132-G-C		Ehlers-Danlos syndrome, spondylocheirodysplastic type	Uncertain significance (May 17, 2021)
11-47410132-G-T		Ehlers-Danlos syndrome, spondylocheirodysplastic type	Uncertain significance (Aug 24, 2021)
11-47410133-C-T		Ehlers-Danlos syndrome, spondylocheirodysplastic type	Likely benign (Dec 24, 2021)
11-47410145-C-T		Ehlers-Danlos syndrome, spondylocheirodysplastic type	Likely benign (Jan 04, 2024)
11-47410149-C-T		Ehlers-Danlos syndrome, spondylocheirodysplastic type	Uncertain significance (Aug 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC39A13	protein_coding	protein_coding	ENST00000362021	9	9365

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00251	0.984	125707	0	29	125736	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.26	170	223	0.763	0.0000146	2347
Missense in Polyphen		48	74.657	0.64294		851
Synonymous	-0.275	108	104	1.03	0.00000768	819
Loss of Function	2.16	7	16.4	0.426	8.04e-7	181

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000249	0.000246
Ashkenazi Jewish	0.00	0.00
East Asian	0.000224	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000143	0.000141
Middle Eastern	0.000224	0.000217
South Asian	0.000131	0.000131
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a zinc-influx transporter. {ECO:0000269|PubMed:21917916}.
• Disease: DISEASE: Ehlers-Danlos syndrome, spondylodysplastic type, 3 (EDSSPD3) [MIM:612350]: A form of Ehlers-Danlos syndrome, a group of connective tissue disorders characterized by skin hyperextensibility, articular hypermobility, and tissue fragility. EDSSPD3 is an autosomal recessive form characterized by a generalized skeletal dysplasia involving mainly the spine and striking clinical abnormalities of the hands, in addition to classic features of Ehlers-Danlos syndrome. Clinical features include postnatal growth retardation, moderate short stature, protuberant eyes with bluish sclerae, hands with finely wrinkled palms, atrophy of the thenar muscles, and tapering fingers. Radiologic features include mild to moderate platyspondyly, mild to moderate osteopenia of the spine, small ileum, flat proximal femoral epiphyses, short, wide femoral necks, and broad metaphyses (elbows, knees, wrists, and interphalangeal joints). {ECO:0000269|PubMed:18513683}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Nuclear Receptors Meta-Pathway;NRF2 pathway;Zinc homeostasis (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.656
• rvis_EVS: 0.98
• rvis_percentile_EVS: 90.38

Haploinsufficiency Scores

• pHI: 0.308
• hipred: N
• hipred_score: 0.242
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.485

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc39a13
• Phenotype: cellular 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; skeleton phenotype; vision/eye phenotype

Gene ontology

• Biological process: cellular zinc ion homeostasis;response to zinc ion;connective tissue development;zinc ion transmembrane transport
• Cellular component: endoplasmic reticulum;Golgi apparatus;integral component of membrane;integral component of Golgi membrane;perinuclear region of cytoplasm
• Molecular function: zinc ion transmembrane transporter activity;protein binding;protein homodimerization activity