SLC39A13

Summary

SLC39A13 (solute carrier family 39 member 13, HGNC:20859) is a protein-coding gene on chromosome 11p11.2, encoding Zinc transporter ZIP13 (Q96H72). Functions as a zinc transporter transporting Zn(2+) from the Golgi apparatus to the cytosol and thus influences the zinc level at least in areas of the cytosol.

This gene encodes a member of the LIV-1 subfamily of the ZIP transporter family. The encoded transmembrane protein functions as a zinc transporter. Mutations in this gene have been associated with the spondylocheiro dysplastic form of Ehlers-Danlos syndrome. Alternate transcript variants have been found for this gene.

Source: NCBI Gene 91252 — RefSeq curated summary.

At a glance

• Gene–disease (curated): Ehlers-Danlos syndrome, spondylocheirodysplastic type (Definitive, ClinGen)
• GWAS associations: 35
• Clinical variants (ClinVar): 415 total — 1 pathogenic, 1 likely-pathogenic
• Phenotypes (HPO): 45
• MANE Select transcript: NM_001128225

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20859
Approved symbol	SLC39A13
Name	solute carrier family 39 member 13
Location	11p11.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ25785, LZT-Hs9, ZIP13, ZIP-13
Ensembl gene	ENSG00000165915
Ensembl biotype	protein_coding
OMIM	608735
Entrez	91252

Gene structure

Transcript identifiers

Ensembl transcripts: 35 — 31 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000354884, ENST00000362021, ENST00000524886, ENST00000524928, ENST00000526614, ENST00000527091, ENST00000527829, ENST00000528979, ENST00000529740, ENST00000531419, ENST00000531865, ENST00000531974, ENST00000533076, ENST00000869741, ENST00000869742, ENST00000869743, ENST00000869744, ENST00000869745, ENST00000869746, ENST00000869747, ENST00000911862, ENST00000911863, ENST00000911864, ENST00000911865, ENST00000911866, ENST00000968891, ENST00000968892, ENST00000968893, ENST00000968894, ENST00000968895, ENST00000968896, ENST00000968897, ENST00000968898, ENST00000968899, ENST00000968900

RefSeq mRNA: 3 — MANE Select: NM_001128225 NM_001128225, NM_001330245, NM_152264

CCDS: CCDS44592, CCDS7934, CCDS81564

Canonical transcript exons

ENST00000362021 — 10 exons

Exon	Start	End
ENSE00001098071	47412346	47412467
ENSE00001098075	47413597	47413686
ENSE00001098077	47414425	47414475
ENSE00001521372	47410087	47410395
ENSE00001521375	47415288	47416496
ENSE00001762114	47415039	47415159
ENSE00002183733	47408590	47408662
ENSE00003662144	47413400	47413507
ENSE00003688356	47414777	47414909
ENSE00003786577	47411926	47412039

Expression profiles

Bgee: expression breadth ubiquitous, 248 present calls, max score 97.47.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.5608 / max 118.4096, expressed in 1810 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
114216	16.6030	1788
114215	2.5758	1234
114189	0.7489	297
114217	0.3452	163
114214	0.2878	133

Top tissues by expression

254 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
metanephros cortex	UBERON:0010533	97.47	gold quality
ascending aorta	UBERON:0001496	96.48	gold quality
thoracic aorta	UBERON:0001515	96.44	gold quality
apex of heart	UBERON:0002098	96.31	gold quality
right coronary artery	UBERON:0001625	96.30	gold quality
right testis	UBERON:0004534	96.27	gold quality
lower esophagus muscularis layer	UBERON:0035833	96.26	gold quality
lower esophagus	UBERON:0013473	96.21	gold quality
body of uterus	UBERON:0009853	96.13	gold quality
aorta	UBERON:0000947	95.91	gold quality
sperm	CL:0000019	95.88	gold quality
stromal cell of endometrium	CL:0002255	95.81	gold quality
left testis	UBERON:0004533	95.76	gold quality
descending thoracic aorta	UBERON:0002345	95.69	gold quality
popliteal artery	UBERON:0002250	95.66	gold quality
tibial artery	UBERON:0007610	95.65	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	95.62	gold quality
left coronary artery	UBERON:0001626	95.49	gold quality
left uterine tube	UBERON:0001303	95.20	gold quality
right hemisphere of cerebellum	UBERON:0014890	95.09	gold quality
coronary artery	UBERON:0001621	94.88	gold quality
upper lobe of left lung	UBERON:0008952	94.87	gold quality
tibial nerve	UBERON:0001323	94.71	gold quality
right ovary	UBERON:0002118	94.69	gold quality
mucosa of stomach	UBERON:0001199	94.67	gold quality
adenohypophysis	UBERON:0002196	94.58	gold quality
endocervix	UBERON:0000458	94.48	gold quality
right lobe of thyroid gland	UBERON:0001119	94.39	gold quality
right atrium auricular region	UBERON:0006631	94.30	gold quality
cerebellar hemisphere	UBERON:0002245	94.28	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.17
E-MTAB-6678	yes	4.73

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

56 targeting SLC39A13, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-512-3P	99.97	67.35	1049
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-6857-5P	99.87	65.32	985
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-6817-3P	99.79	68.35	2126
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-1296-3P	99.72	64.04	636
HSA-MIR-1200	99.71	70.42	1838
HSA-MIR-7150	99.62	66.80	1322
HSA-MIR-6836-5P	99.60	65.62	1538
HSA-MIR-6132	99.60	65.83	1554
HSA-MIR-12122	99.56	69.33	1672
HSA-MIR-5584-5P	99.49	68.22	2814
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-135A-5P	99.36	71.85	1601

Literature-anchored findings (GeneRIF, showing 9)

• clinical features of 6 patients from 2 consanguineous families with Ehlers-Danlos syndrome-like features caused by a mutation in the zinc transporter gene SLC39A13 (PMID:18513683)
• mutations in the SLC39A13 gene do not account for the Ehlers-Danlos syndrome type VIB phenotype (PMID:21739577)
• Biochemical characterization of human ZIP13 protein: a homo-dimerized zinc transporter involved in the spondylocheiro dysplastic Ehlers-Danlos syndrome. (PMID:21917916)
• human ZIP13 releases zinc from vesicular stores (PMID:23213233)
• The spondylocheiro dysplastic form of Ehlers-Danlos syndrome, in which ZIP13 is defective, is likely due to a failure of iron delivery to the secretory compartments. (PMID:25006035)
• Authors demonstrated that both the ZIP13(G64D) and ZIP13(DeltaFLA) protein levels are decreased by degradation via the valosin-containing protein (VCP)-linked ubiquitin proteasome pathway. (PMID:25007800)
• The Connective Tissue Disorder Associated with Recessive Variants in the SLC39A13 Zinc Transporter Gene (Spondylo-Dysplastic Ehlers-Danlos Syndrome Type 3): Insights from Four Novel Patients and Follow-Up on Two Original Cases. (PMID:32295219)
• Zinc transporter SLC39A13/ZIP13 facilitates the metastasis of human ovarian cancer cells via activating Src/FAK signaling pathway. (PMID:34154618)
• Possible involvement of zinc transporter ZIP13 in myogenic differentiation. (PMID:38609428)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	slc39a13	ENSDARG00000000442
mus_musculus	Slc39a13	ENSMUSG00000002105
rattus_norvegicus	Slc39a13	ENSRNOG00000011981
drosophila_melanogaster	Zip99C	FBGN0039714
caenorhabditis_elegans		WBGENE00007591

Paralogs (1): SLC39A7 (ENSG00000112473)

Protein

Protein identifiers

Zinc transporter ZIP13 — Q96H72 (reviewed: Q96H72)

Alternative names: LIV-1 subfamily of ZIP zinc transporter 9, Solute carrier family 39 member 13, Zrt- and Irt-like protein 13

All UniProt accessions (8): Q96H72, E9PNE7, E9PNN7, E9PRH4, E9PSA8, G3V1B2, K4DIA9, K4DIB5

UniProt curated annotations — full annotation on UniProt →

Function. Functions as a zinc transporter transporting Zn(2+) from the Golgi apparatus to the cytosol and thus influences the zinc level at least in areas of the cytosol. May regulate beige adipocyte differentiation.

Subunit / interactions. Homodimer.

Subcellular location. Golgi apparatus membrane. Cytoplasmic vesicle membrane. Endoplasmic reticulum membrane.

Disease relevance. 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). The disease is caused by variants affecting the gene represented in this entry.

Induction. Up-regulated under zinc-limiting conditions. Induces by TGFB1.

Similarity. Belongs to the ZIP transporter (TC 2.A.5) family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96H72-1	1	yes
Q96H72-2	2

RefSeq proteins (3): NP_001121697, NP_001317174, NP_689477 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003689	ZIP	Family

Pfam: PF02535

Catalyzed reactions (Rhea), 1 shown:

• Zn(2+)(in) = Zn(2+)(out) (RHEA:29351)

UniProt features (24 total): topological domain 9, transmembrane region 8, sequence variant 4, chain 1, short sequence motif 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96H72-F1	76.33	0.38

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 301 (showing top): GOBP_TRANSITION_METAL_ION_TRANSPORT, GOZGIT_ESR1_TARGETS_DN, AAGCCAT_MIR135A_MIR135B, DARWICHE_SKIN_TUMOR_PROMOTER_DN, DARWICHE_PAPILLOMA_RISK_LOW_DN, DARWICHE_PAPILLOMA_RISK_HIGH_DN, DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN, CEBPB_01, GOBP_MONOATOMIC_CATION_TRANSPORT, TGCTGAY_UNKNOWN, BACH2_01, GOBP_BROWN_FAT_CELL_DIFFERENTIATION, E4F1_Q6, TGANTCA_AP1_C, GOBP_FAT_CELL_DIFFERENTIATION

GO Biological Process (8): zinc ion transport (GO:0006829), intracellular zinc ion homeostasis (GO:0006882), brown fat cell differentiation (GO:0050873), connective tissue development (GO:0061448), zinc ion transmembrane transport (GO:0071577), monoatomic ion transport (GO:0006811), metal ion transport (GO:0030001), transmembrane transport (GO:0055085)

GO Molecular Function (4): zinc ion transmembrane transporter activity (GO:0005385), protein homodimerization activity (GO:0042803), protein binding (GO:0005515), metal ion transmembrane transporter activity (GO:0046873)

GO Cellular Component (8): Golgi membrane (GO:0000139), endoplasmic reticulum membrane (GO:0005789), Golgi apparatus (GO:0005794), membrane (GO:0016020), cytoplasmic vesicle membrane (GO:0030659), perinuclear region of cytoplasm (GO:0048471), endoplasmic reticulum (GO:0005783), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	4
transport	2
endomembrane system	2
intracellular membrane-bounded organelle	2
cellular anatomical structure	2
transition metal ion transport	1
intracellular monoatomic cation homeostasis	1
inorganic ion homeostasis	1
fat cell differentiation	1
tissue development	1
zinc ion transport	1
monoatomic cation transmembrane transport	1
monoatomic cation transport	1
cellular process	1
transition metal ion transmembrane transporter activity	1
zinc ion transmembrane transport	1
identical protein binding	1
protein dimerization activity	1
binding	1
monoatomic cation transmembrane transporter activity	1
metal ion transport	1
Golgi apparatus	1
bounding membrane of organelle	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
vesicle membrane	1
cytoplasmic vesicle	1
intracellular vesicle	1

Protein interactions and networks

STRING

1020 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC39A13	SLC39A9	Q9NUM3	841
SLC39A13	SLC39A11	Q8N1S5	805
SLC39A13	SLC30A2	Q9BRI3	795
SLC39A13	SLC30A5	Q8TAD4	789
SLC39A13	SLC39A1	Q9NY26	774
SLC39A13	SLC30A7	Q8NEW0	770
SLC39A13	SLC30A4	O14863	759
SLC39A13	SLC30A6	Q6NXT4	754
SLC39A13	SLC30A1	Q9Y6M5	725
SLC39A13	SLC30A9	Q6PML9	711
SLC39A13	SLC30A10	Q6XR72	677
SLC39A13	SLC30A3	Q99726	674
SLC39A13	SLC39A2	Q9NP94	652
SLC39A13	SLC39A3	Q9BRY0	649
SLC39A13	B4GALT7	Q9UBV7	641
SLC39A13	FKBP14	Q9NWM8	641

IntAct

21 interactions, top by confidence:

A	B	Type	Score
TCF4	SLC39A13	psi-mi:“MI:0915”(physical association)	0.560
SLC39A13	REL	psi-mi:“MI:0915”(physical association)	0.560
SLC39A13	TCF4	psi-mi:“MI:0915”(physical association)	0.560
REL	SLC39A13	psi-mi:“MI:0915”(physical association)	0.560
	SLC39A13	psi-mi:“MI:0915”(physical association)	0.560
CD40	SLC39A13	psi-mi:“MI:0915”(physical association)	0.560
PGRMC2	SLC39A13	psi-mi:“MI:0915”(physical association)	0.560
MAPK8IP2	SLC39A13	psi-mi:“MI:0915”(physical association)	0.370
SLC39A13	F2RL1	psi-mi:“MI:0915”(physical association)	0.370
SLC39A13	OPRM1	psi-mi:“MI:0915”(physical association)	0.370
KIR2DL4	GPR89A	psi-mi:“MI:0914”(association)	0.350
SLC39A13	SCO1	psi-mi:“MI:0914”(association)	0.350
SLC39A13		psi-mi:“MI:0915”(physical association)	0.000
SLC39A13	CD40	psi-mi:“MI:0915”(physical association)	0.000
SLC39A13	PGRMC2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (52): SLC39A13 (Two-hybrid), SLC39A13 (Two-hybrid), SLC39A13 (Two-hybrid), SLC39A13 (Two-hybrid), SLC39A13 (Two-hybrid), SLC39A13 (Two-hybrid), SLC39A13 (Two-hybrid), SLC39A13 (Two-hybrid), SLC39A13 (Two-hybrid), SLC39A13 (Affinity Capture-RNA), SLC39A13 (Affinity Capture-MS), SLC39A13 (Negative Genetic), SLC39A13 (Proximity Label-MS), ABI1 (Affinity Capture-MS), AKAP12 (Affinity Capture-MS)

ESM2 similar proteins: A2AIG8, A5D7H1, A6H7A0, A6NFX1, A6NJW4, A8MUP2, A8MXK1, B0BMW8, O35393, O54804, O73884, P01135, P35790, P52875, P57791, Q00961, Q01098, Q01134, Q06922, Q08DW9, Q0P5M9, Q0VDI3, Q14728, Q14957, Q15768, Q2M1K6, Q3UGX3, Q4R7M4, Q4V899, Q5E9H2, Q5M7U7, Q5R6I6, Q5RCI5, Q5ZI20, Q7TPB4, Q8BZH0, Q8IVW8, Q8N431, Q8NBA8, Q8R2R5

Diamond homologs: A0A0G2KQY6, A0A6I8PMZ8, A4IGY6, A5D7H1, A5D7L5, A8WMY3, A8X482, L5KLU7, P0DX17, Q06916, Q15043, Q1KZG0, Q29175, Q2M1K6, Q31125, Q504Y0, Q5FVQ0, Q5FWH7, Q5R6I6, Q5RAB7, Q5RFD5, Q5TJF6, Q6L8F3, Q6MGB4, Q6P5F6, Q6PEH9, Q75N73, Q78IQ7, Q8AW42, Q8BZH0, Q91W10, Q92504, Q96H72, Q9C0K1, Q9M647, Q9PUB8, Q9ULF5, Q9UT11, Q9V3A4, Q9XTQ7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

415 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	1
Uncertain significance	145
Likely benign	204
Benign	21

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
2132	NM_001128225.3(SLC39A13):c.483_491del (p.Phe162_Ala164del)	Pathogenic
1175795	NM_001128225.3(SLC39A13):c.598C>T (p.Gln200Ter)	Likely pathogenic

SpliceAI

1763 predictions. Top by Δscore:

Variant	Effect	Δscore
11:47410086:GTAC:G	acceptor_gain	1.0000
11:47410249:A:T	donor_gain	1.0000
11:47410392:GAAG:G	donor_gain	1.0000
11:47410395:GGTA:G	donor_loss	1.0000
11:47410396:G:C	donor_loss	1.0000
11:47410397:T:G	donor_loss	1.0000
11:47411920:TTGTA:T	acceptor_loss	1.0000
11:47411921:TGTA:T	acceptor_loss	1.0000
11:47411923:TA:T	acceptor_loss	1.0000
11:47411924:A:AC	acceptor_loss	1.0000
11:47411924:A:AG	acceptor_gain	1.0000
11:47411924:AGCT:A	acceptor_gain	1.0000
11:47411924:AGCTG:A	acceptor_gain	1.0000
11:47411925:G:GG	acceptor_gain	1.0000
11:47411925:GC:G	acceptor_gain	1.0000
11:47411925:GCT:G	acceptor_gain	1.0000
11:47411925:GCTG:G	acceptor_gain	1.0000
11:47411925:GCTGG:G	acceptor_gain	1.0000
11:47412037:CTG:C	donor_gain	1.0000
11:47412037:CTGG:C	donor_loss	1.0000
11:47412038:TG:T	donor_gain	1.0000
11:47412038:TGGTA:T	donor_loss	1.0000
11:47412039:GG:G	donor_gain	1.0000
11:47412040:G:GG	donor_gain	1.0000
11:47412041:T:G	donor_loss	1.0000
11:47413391:T:TA	acceptor_gain	1.0000
11:47413392:G:A	acceptor_gain	1.0000
11:47413395:CCTA:C	acceptor_loss	1.0000
11:47413397:TA:T	acceptor_loss	1.0000
11:47413398:A:AG	acceptor_gain	1.0000

AlphaMissense

2371 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:47413638:C:A	N229K	0.998
11:47413638:C:G	N229K	0.998
11:47413649:G:A	G233E	0.998
11:47413666:A:C	S239R	0.998
11:47413668:C:A	S239R	0.998
11:47413668:C:G	S239R	0.998
11:47413669:T:C	F240L	0.998
11:47413671:C:A	F240L	0.998
11:47413671:C:G	F240L	0.998
11:47414429:G:A	G247E	0.998
11:47414784:A:C	D265A	0.998
11:47414784:A:T	D265V	0.998
11:47413634:A:T	D228V	0.997
11:47413648:G:T	G233W	0.997
11:47414462:A:T	E258V	0.997
11:47414784:A:G	D265G	0.997
11:47414785:C:A	D265E	0.997
11:47414785:C:G	D265E	0.997
11:47414786:T:C	F266L	0.997
11:47414788:T:A	F266L	0.997
11:47414788:T:G	F266L	0.997
11:47410314:G:C	G74R	0.996
11:47413634:A:C	D228A	0.996
11:47414783:G:C	D265H	0.996
11:47414796:T:C	L269P	0.996
11:47414804:G:C	A272P	0.996
11:47414868:G:A	G293D	0.996
11:47410315:G:A	G74D	0.995
11:47410335:A:C	S81R	0.995
11:47410337:T:A	S81R	0.995

dbSNP variants (sampled 300 via entrez): RS1000158256 (11:47407830 A>G), RS1000286276 (11:47407522 A>G), RS1000304482 (11:47416373 G>A), RS1000885409 (11:47410419 C>T), RS1001091101 (11:47414655 A>G), RS1001109414 (11:47409192 A>G), RS1001399862 (11:47407356 A>G), RS1001426267 (11:47413325 C>T), RS1001469694 (11:47408613 C>G,T), RS1001793548 (11:47411402 C>T), RS1002168038 (11:47405599 G>T), RS1002713031 (11:47407723 G>A), RS1003096724 (11:47411739 ATGGTGGT>A), RS1003215877 (11:47406985 G>C), RS1003430446 (11:47410397 T>C)

Disease associations

OMIM: gene MIM:608735 | disease phenotypes: MIM:612350, MIM:130000, MIM:160700, MIM:601353

GenCC curated gene-disease

Disease	Classification	Inheritance
Ehlers-Danlos syndrome, spondylocheirodysplastic type	Definitive	Autosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
Ehlers-Danlos syndrome, spondylocheirodysplastic type	Definitive	AR

Mondo (8): Ehlers-Danlos syndrome, spondylocheirodysplastic type (MONDO:0012873), connective tissue disorder (MONDO:0003900), Ehlers-Danlos syndrome (MONDO:0020066), myopia (MONDO:0001384), mitral valve prolapse (MONDO:0004910), cutis laxa (MONDO:0016175), scleroderma (MONDO:0019340), Fine-Lubinsky syndrome (MONDO:0011049)

Orphanet (5): SLC39A13-related spondylodysplastic Ehlers-Danlos syndrome (Orphanet:157965), Ehlers-Danlos syndrome (Orphanet:98249), Cutis laxa (Orphanet:209), Scleroderma (Orphanet:801), Aymé-Gripp syndrome (Orphanet:1272)

HPO phenotypes

45 total (30 of 45 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000193	Bifid uvula
HP:0000218	High palate
HP:0000316	Hypertelorism
HP:0000465	Webbed neck
HP:0000494	Downslanted palpebral fissures
HP:0000520	Proptosis
HP:0000592	Blue sclerae
HP:0000668	Hypodontia
HP:0000684	Delayed eruption of teeth
HP:0000689	Dental malocclusion
HP:0000926	Platyspondyly
HP:0000938	Osteopenia
HP:0000944	Abnormal metaphysis morphology
HP:0000963	Thin skin
HP:0000974	Hyperextensible skin
HP:0000978	Bruising susceptibility
HP:0001015	Prominent superficial veins
HP:0001073	Cigarette-paper scars
HP:0001182	Tapered finger
HP:0001270	Motor delay
HP:0001371	Flexion contracture
HP:0001382	Joint hypermobility
HP:0001508	Failure to thrive
HP:0001763	Pes planus
HP:0002007	Frontal bossing
HP:0002515	Waddling gait
HP:0002652	Skeletal dysplasia
HP:0002751	Kyphoscoliosis
HP:0003015	Flared metaphysis

GWAS associations

35 associations (top):

Study	Trait	p-value
GCST004065_10	Waist circumference	9.000000e-10
GCST004065_51	Waist circumference	2.000000e-08
GCST004066_114	Hip circumference	2.000000e-09
GCST004066_12	Hip circumference	6.000000e-06
GCST004066_41	Hip circumference	2.000000e-06
GCST004776_59	Systolic blood pressure	3.000000e-07
GCST004777_25	Diastolic blood pressure	7.000000e-08
GCST005232_56	Neuroticism	1.000000e-16
GCST005905_14	Global electrical heterogeneity phenotypes	6.000000e-09
GCST006258_12	Diastolic blood pressure	9.000000e-19
GCST006259_19	Systolic blood pressure	4.000000e-13
GCST006716_13	Alcohol use disorder (total score)	6.000000e-09
GCST006923_11	Loneliness	1.000000e-07
GCST006924_13	Loneliness (MTAG)	1.000000e-08
GCST007267_68	Systolic blood pressure	1.000000e-21
GCST007293_118	Body fat distribution (arm fat ratio)	3.000000e-08
GCST007293_19	Body fat distribution (arm fat ratio)	2.000000e-10
GCST007293_45	Body fat distribution (arm fat ratio)	5.000000e-14
GCST007294_28	Body fat distribution (trunk fat ratio)	6.000000e-09
GCST007294_9	Body fat distribution (trunk fat ratio)	4.000000e-06
GCST007295_159	Body fat distribution (leg fat ratio)	1.000000e-18
GCST007295_24	Body fat distribution (leg fat ratio)	7.000000e-08
GCST007295_50	Body fat distribution (leg fat ratio)	2.000000e-12
GCST007825_4	Alzheimer’s disease or fasting glucose levels (pleiotropy)	3.000000e-16
GCST007876_93	Estimated glomerular filtration rate	1.000000e-11
GCST008058_91	Estimated glomerular filtration rate	1.000000e-20
GCST008060_44	Estimated glomerular filtration rate	4.000000e-06
GCST008062_93	Blood urea nitrogen levels	2.000000e-06
GCST008064_9	Chronic kidney disease	3.000000e-07
GCST010002_238	Refractive error	2.000000e-14

EFO canonical traits (9, from GWAS)

EFO ID	Trait name
EFO:0006335	systolic blood pressure
EFO:0006336	diastolic blood pressure
EFO:0007660	neuroticism measurement
EFO:0004327	electrocardiography
EFO:0009458	alcohol use disorder measurement
EFO:0007865	loneliness measurement
EFO:0004341	body fat distribution
EFO:0008111	diet measurement
EFO:0004346	neuroimaging measurement

MeSH disease descriptors (7)

Descriptor	Name	Tree numbers
D003240	Connective Tissue Diseases	C17.300
D003483	Cutis Laxa	C16.320.850.180; C17.300.230; C17.800.827.180
D004535	Ehlers-Danlos Syndrome	C14.907.454.240; C15.378.463.515.240; C16.131.831.428; C16.320.850.260; C17.300.200.310; C17.800.804.428; C17.800.827.260
D008945	Mitral Valve Prolapse	C14.280.484.400.500
D009216	Myopia	C11.744.636
C537933	Fine-Lubinsky syndrome (supp.)
C567340	Spondylocheirodysplasia, Ehlers-Danlos Syndrome-Like (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: transporter — SLC39 family of metal ion transporters

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	decreases expression	1
triphenyl phosphate	affects expression	1
sodium arsenite	increases expression	1
cobaltous chloride	decreases expression	1
cupric chloride	increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
Grape Seed Proanthocyanidins	increases expression	1
jinfukang	increases expression	1
Arsenic Trioxide	decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Calcitriol	decreases expression	1
Doxorubicin	affects expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Zinc	increases transport	1
Acrylamide	decreases expression	1
Vitamin K 3	affects expression	1
Particulate Matter	increases expression	1

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_D4NE	HCT116-SLC39A13-KO-c5	Cancer cell line	Male
CVCL_D4NF	HCT116-SLC39A13-KO-c6	Cancer cell line	Male
CVCL_TN53	HAP1 SLC39A13 (-) 1	Cancer cell line	Male
CVCL_XT30	HAP1 SLC39A13 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

282 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT01042158	PHASE4	COMPLETED	A Clinical Trial of Ambrisentan and Tadalafil in Pulmonary Arterial Hypertension Associated With Systemic Sclerosis
NCT03688191	PHASE4	UNKNOWN	Study of Sirolimus in CTD-TP in China
NCT04169100	PHASE4	UNKNOWN	Novel Form of Acquired Long QT Syndrome
NCT04197050	PHASE4	UNKNOWN	Effect of Sacubitril/Valsartan on Reduced Right Ventricular Ejection Fraction in Patients With CTD
NCT04928586	PHASE4	UNKNOWN	Immunosuppressant Combined With Pirfenidone in CTD-ILD
NCT05440240	PHASE4	RECRUITING	Percutaneous Needle Fasciotomy +/- Corticosteroid Injection for Dupuytren’s Contracture
NCT05505409	PHASE4	UNKNOWN	Efficacy and Safety of Pirfenidone in CTD-ILD
NCT06499233	PHASE4	RECRUITING	Efficacy and Safety of Prophylactic Treatment for Pneumocystis Jirovecii Pneumonia in Patients With Autoimmune Inflammatory Rheumatic Disease
NCT04890431	PHASE4	UNKNOWN	Impact of Oxygen Therapy on Fatigue in Patients With Hypermobile-type Ehlers-Danlos Syndrome
NCT05603741	PHASE4	ACTIVE_NOT_RECRUITING	Local Anesthetic Response in Ehlers-Danlos Syndrome (EDS) and Healthy Volunteers
NCT00347204	PHASE4	COMPLETED	Comparison of Acular LS Versus Nevanac for Pain Control in Eyes Undergoing PRK
NCT00349843	PHASE4	COMPLETED	Investigation of Multi-Purpose Solution-Based Corneal Staining and Ocular Comfort
NCT00349882	PHASE4	COMPLETED	Effects of Contact Lens Care Regimens on the Corneal Epithelium
NCT00350246	PHASE4	COMPLETED	Long-term Effects of Laser Refractive Surgery
NCT00404105	PHASE4	COMPLETED	A Comparison of PRK and LASIK for Correction of Myopia
NCT00455455	PHASE4	COMPLETED	Corneal and Conjunctival Sensitivity and Staining Study
NCT00541177	PHASE4	UNKNOWN	Study of Myopia Prevention in Children With Low Concentration of Atropine
NCT00627302	PHASE4	COMPLETED	Efficacy of PEG-400 and Systane Artificial Tears (Alcon) on Quality of Vision
NCT00640341	PHASE4	COMPLETED	Comparative Performance of PureVision, Acuvue Oasys and O2Optix
NCT00770094	PHASE4	UNKNOWN	Multi Laser Platform Comparison Study for LASIK
NCT00821236	PHASE4	COMPLETED	Contralateral Comparison of Three Excimer Laser Systems in Performing LASIK
NCT00889941	PHASE4	COMPLETED	Effect of Preoperative Pupil Size on Quality of Vision After Wavefront-Guided LASIK
NCT00937105	PHASE4	COMPLETED	Daily Wear Corneal Infiltrative Event Study
NCT01173198	PHASE4	COMPLETED	An Evaluation of Outcomes Following Wavefront Optimized or Wavefront Guided Lasik Procedure in Low to Moderate Myopic Patients
NCT01250925	PHASE4	COMPLETED	Effect of Contact Lens Wear on Immune Cell Density and Morphology of the Ocular Surface
NCT01387360	PHASE4	COMPLETED	Presbyopic Supracor Treatment for Near Myopic/Hyperopic Pseudophakic Eyes
NCT01454843	PHASE4	COMPLETED	LASIK Using the Alcon Allegretto Wavefront-Guided Excimer Laser vs AMO Visx Wavefront-Guided Excimer Laser
NCT01693939	PHASE4	COMPLETED	Evaluation of the Post-LASIK Flap Thickness of the FS200 Femtosecond Laser Flap
NCT01706237	PHASE4	WITHDRAWN	Visual Outcomes And Contrast Sensitivity After Myopic Wavefront-Optimized Lasik With Nexisvision Shield Or Bandage Contact Lens
NCT01746589	PHASE4	COMPLETED	Visual Outcomes and Contrast Sensitivity After Myopic LASIK
NCT01977807	PHASE4	UNKNOWN	A Prospective Safety and Effectiveness Study of the 500 Hz Technolas Perfect Vision Excimer Laser in Asian Eyes Using LASIK
NCT02071576	PHASE4	UNKNOWN	A Prospective Safety and Effectiveness Study of the 500 Hz Technolas Perfect Vision Excimer Laser Using LASIK
NCT02112968	PHASE4	UNKNOWN	A Prospective Safety and Effectiveness Study of a New High Repetition Rate Excimer Laser Using LASIK for the Correction of Ammetropia and Presbyopia
NCT02186184	PHASE4	COMPLETED	Effect of Orthokeratology Versus Spectacles on Myopia Progression in Chinese Children: A Crossover Trial
NCT02544529	PHASE4	WITHDRAWN	Echothiophate Iodide for the Prevention of Progression of Myopia
NCT03001401	PHASE4	UNKNOWN	Comparison of Next Generation Laser Techniques of Myopia Correction: iDesign vs. SMILE
NCT03158142	PHASE4	COMPLETED	The Influence of Atropine on Choroidal Thickness
NCT03544827	PHASE4	COMPLETED	The Effects of Low Dose Atropine on Choroidal Thickness
NCT03881670	PHASE4	COMPLETED	On-Eye Optical Quality of Lotrafilcon B Lenses Over 12 Hours
NCT03949101	PHASE4	UNKNOWN	Atropine for Children and Adolescent Myopia Progression Study