Myopia 24, autosomal dominant

Summary

Myopia 24, autosomal dominant (MONDO:0014411) is a disease caused by SLC39A5 (GenCC Strong), with 1 cohort gene.

At a glance

• Causal gene: SLC39A5 (GenCC Strong)
• Cohort genes: 1
• ClinVar variants: 13

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	myopia 24, autosomal dominant
Mondo ID	MONDO:0014411
OMIM	615946
UMLS	C4014762
MedGen	863199
Is cancer (heuristic)	no

Also known as: myopia 24, autosomal dominant · MYP24

Data availability: 13 ClinVar variants · 3 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary disease › myopia › myopia 24, autosomal dominant

Related subtypes (29): degenerative myopia, myopia 2, autosomal dominant, myopia 18, autosomal recessive, myopia 13, X-linked, myopia 1, X-linked, myopia 3, autosomal dominant, myopia 17, autosomal dominant, myopia 5, autosomal dominant, myopia 6, myopia 7, myopia 8, myopia 9, myopia 10, myopia 11, autosomal dominant, myopia 12, autosomal dominant, myopia 14, myopia 16, autosomal dominant, myopia 15, autosomal dominant, schizophrenia 16, myopia 19, autosomal dominant, myopia 20, autosomal dominant, myopia 21, autosomal dominant, myopia, high, with cataract and vitreoretinal degeneration, myopia 22, autosomal dominant, myopia 23, autosomal recessive, myopia 25, autosomal dominant, myopia 28, autosomal recessive, myopia 27, myopia 26, X-linked, female-limited

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

13 retrieved; paginated sample, class counts are floors:

6 uncertain significance, 2 likely pathogenic, 2 conflicting classifications of pathogenicity, 1 benign, 1 benign/likely benign, 1 pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
143992	NM_173596.3(SLC39A5):c.911T>C (p.Met304Thr)	SLC39A5	Pathogenic	no assertion criteria provided
1285407	NM_173596.3(SLC39A5):c.227dup (p.Gln77fs)	SLC39A5	Likely pathogenic	criteria provided, single submitter
143991	NM_173596.3(SLC39A5):c.141C>G (p.Tyr47Ter)	SLC39A5	Likely pathogenic	criteria provided, single submitter
3319767	NM_173596.3(SLC39A5):c.818G>A (p.Arg273Gln)	SLC39A5	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
3765635	NM_173596.3(SLC39A5):c.1128del (p.His377fs)	SLC39A5	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
2436028	NM_173596.3(SLC39A5):c.964C>T (p.Arg322Ter)	SLC39A5	Uncertain significance	criteria provided, multiple submitters, no conflicts
3065875	NM_173596.3(SLC39A5):c.1495C>T (p.Arg499Cys)	SLC39A5	Uncertain significance	criteria provided, single submitter
3319766	NM_173596.3(SLC39A5):c.822C>G (p.His274Gln)	SLC39A5	Uncertain significance	criteria provided, multiple submitters, no conflicts
3780623	NM_173596.3(SLC39A5):c.471+1G>A	SLC39A5	Uncertain significance	criteria provided, single submitter
3780624	NM_173596.3(SLC39A5):c.804+1G>A	SLC39A5	Uncertain significance	criteria provided, single submitter
3780625	NM_173596.3(SLC39A5):c.1479+2_1479+5del	SLC39A5	Uncertain significance	criteria provided, single submitter
1333138	NM_173596.3(SLC39A5):c.-14T>C	SLC39A5	Benign	criteria provided, multiple submitters, no conflicts
1333139	NM_173596.3(SLC39A5):c.1121G>C (p.Ser374Thr)	SLC39A5	Benign/Likely benign	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 3 · Orphanet: 1 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

Gene	Classification	Inheritance	Disease	Records
SLC39A5	Strong	Autosomal dominant	myopia 24, autosomal dominant	3

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
SLC39A5	Orphanet:98619	Rare isolated myopia

Cohort genes → proteins

1 cohort genes, 1 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	1

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
SLC39A5	HGNC:20502	ENSG00000139540	Q6ZMH5	Zinc transporter ZIP5	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
SLC39A5	Zinc transporter ZIP5	Uniporter that transports zinc(2+) into polarized cells of enterocytes, pancreatic acinar and endoderm cells across the basolateral membrane and participates, notably, in zinc excretion from the intestine by the uptake of zinc from the blo…

Protein-family classification

Druggable: 1 · Difficult: 0 · Unknown: 0 · Druggable fraction: 1.0

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

Family	Genes	Fold	FDR
Transporter	1	77.8×	0.013

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
SLC39A5	Transporter	yes		ZIP, ZIP_Transporter

Expression context

Cohort genes with no expression data: 0.

1 cohort gene are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

Bucket	Genes
narrow (1-5 tissues)	0
moderate (6-20)	0
broad (>20)	1
unknown	0

Top tissues across cohort

Tissue	Cohort genes
body of pancreas	1
mucosa of transverse colon	1
right lobe of liver	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
SLC39A5	165	tissue_specific	marker	body of pancreas, mucosa of transverse colon, right lobe of liver

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
SLC39A5	973

Structural data

PDB: 1 · AlphaFold-only: 0 · No structure: 0

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
SLC39A5	Q6ZMH5	4

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 6. Enrichment computed across 1 evidence-associated genes (1 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

Pathway	Cohort genes	Fold	FDR	Sample cohort genes
Zinc transporters	1	1142.0×	0.003	SLC39A5
Zinc influx into cells by the SLC39 gene family	1	1142.0×	0.003	SLC39A5
Metal ion SLC transporters	1	601.0×	0.003	SLC39A5
R-HSA-425366	1	181.3×	0.008	SLC39A5
SLC-mediated transmembrane transport	1	59.2×	0.020	SLC39A5
Transport of small molecules	1	25.1×	0.040	SLC39A5

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO term	Cohort genes	Fold	FDR	Sample cohort genes
G1 to G0 transition involved in cell differentiation	1	2808.7×	0.002	SLC39A5
cellular response to zinc ion starvation	1	2407.4×	0.002	SLC39A5
zinc ion import across plasma membrane	1	1685.2×	0.002	SLC39A5
zinc ion transport	1	1532.0×	0.002	SLC39A5
intracellular monoatomic cation homeostasis	1	1123.5×	0.002	SLC39A5
zinc ion transmembrane transport	1	702.2×	0.002	SLC39A5
neural precursor cell proliferation	1	674.1×	0.002	SLC39A5
positive regulation of mRNA splicing, via spliceosome	1	543.6×	0.002	SLC39A5
eye development	1	351.1×	0.003	SLC39A5
BMP signaling pathway	1	200.6×	0.005	SLC39A5

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 1

Druggability breadth: 0 of 1 evidence-associated genes (0%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
SLC39A5	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Pharmacogenomics

Cohort genes with a PharmGKB record: 1; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

0 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	0
B	Phased (≥1) drug, not yet approved	0
C	Druggable family + PDB, no drug	1	SLC39A5
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	0

Undrugged target profiles

1 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

Symbol	ChEMBL assays	Drugged partners (top 3)
SLC39A5	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.