Atrophy of testis

Summary

Atrophy of testis (MONDO:0001415) is a disease with 2 cohort genes and 1 clinical trial.

At a glance

• Cohort genes: 2
• ClinVar variants: 3
• Clinical trials: 1

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	atrophy of testis
Mondo ID	MONDO:0001415
DOID	DOID:11994
ICD-10-CM	N50.0
ICD-11	1735709719
NCIT	C123259
SNOMED CT	17585008
UMLS	C0156312
MedGen	57626
Is cancer (heuristic)	no

Also known as: testicular atrophy

Data availability: 3 ClinVar variants.

Disease family

Classification path: disease › human disease › disease by body system or component › reproductive system disorder › gonadal disorder › testicular disorder › atrophy of testis

Related subtypes (7): chylocele of tunica vaginalis, testicular infarct, testicular dysgenesis syndrome, orchitis, spermatic cord torsion, neoplasm of testis, acquired testicular failure

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

3 retrieved; paginated sample, class counts are floors:

1 likely pathogenic, 1 uncertain significance, 1 pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
267800	46;XY;t(7;8)(p12.3;p11.2)dn		Pathogenic	criteria provided, single submitter
1711193	NM_133496.5(SLC30A7):c.842+15T>C	SLC30A7	Likely pathogenic	criteria provided, single submitter
245987	NM_020631.6(PLEKHG5):c.83C>T (p.Pro28Leu)	PLEKHG5	Uncertain significance	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 2 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
PLEKHG5	Orphanet:206580	Autosomal recessive lower motor neuron disease with childhood onset
PLEKHG5	Orphanet:369867	Autosomal recessive intermediate Charcot-Marie-Tooth disease type C

Cohort genes → proteins

2 cohort genes, 2 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	2

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
SLC30A7	HGNC:19306	ENSG00000162695	Q8NEW0	Zinc transporter 7	clinvar
PLEKHG5	HGNC:29105	ENSG00000171680	O94827	Pleckstrin homology domain-containing family G member 5	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
SLC30A7	Zinc transporter 7	Zinc ion transporter mediating zinc entry from the cytosol into the lumen of organelles along the secretory pathway.
PLEKHG5	Pleckstrin homology domain-containing family G member 5	Functions as a guanine exchange factor (GEF) for RAB26 and thus regulates autophagy of synaptic vesicles in axon terminal of motoneurons.

Protein-family classification

Druggable: 0 · Difficult: 1 · Unknown: 1 · Druggable fraction: 0.0

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
Scaffold/PPI	1	8.6×	0.225
Other/Unknown	1	0.9×	0.805

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
SLC30A7	Other/Unknown	no		Cation_efflux, Cation_efflux_TMD_sf, Msc2-like
PLEKHG5	Scaffold/PPI	no		DH_dom, PH_domain, PH-like_dom_sf

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)	2
unknown	0

Top tissues across cohort

Tissue	Cohort genes
buccal mucosa cell	1
oviduct epithelium	1
pancreatic ductal cell	1
cerebellar hemisphere	1
right hemisphere of cerebellum	1
sural nerve	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
SLC30A7	249	ubiquitous	marker	oviduct epithelium, pancreatic ductal cell, buccal mucosa cell
PLEKHG5	175	ubiquitous	yes	sural nerve, right hemisphere of cerebellum, cerebellar hemisphere

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
SLC30A7	1,374
PLEKHG5	966

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
SLC30A7	Q8NEW0	7

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
PLEKHG5	O94827	64.94

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 5. Enrichment computed across 2 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
RND1 GTPase cycle	1	265.6×	0.009	PLEKHG5
RND3 GTPase cycle	1	259.6×	0.009	PLEKHG5
NRAGE signals death through JNK	1	184.2×	0.009	PLEKHG5
G alpha (12/13) signalling events	1	137.6×	0.009	PLEKHG5
RHOA GTPase cycle	1	74.6×	0.013	PLEKHG5

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 2 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO term	Cohort genes	Fold	FDR	Sample cohort genes
zinc ion import into Golgi lumen	1	2808.7×	0.002	SLC30A7
endothelial cell chemotaxis	1	842.6×	0.004	PLEKHG5
intracellular zinc ion homeostasis	1	240.7×	0.009	SLC30A7
endothelial cell migration	1	205.5×	0.009	PLEKHG5
Rho protein signal transduction	1	123.9×	0.011	PLEKHG5
regulation of small GTPase mediated signal transduction	1	72.0×	0.016	PLEKHG5
positive regulation of canonical NF-kappaB signal transduction	1	36.3×	0.027	PLEKHG5

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 2

Druggability breadth: 1 of 2 evidence-associated genes (50%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
SLC30A7	0	0
PLEKHG5	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

Symbol	Assays	Type breakdown
SLC30A7	1	Binding:1

Pharmacogenomics

Cohort genes with a PharmGKB record: 2; 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	0
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	2	SLC30A7, PLEKHG5

Undrugged target profiles

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

Symbol	ChEMBL assays	Drugged partners (top 3)
SLC30A7	1	—
PLEKHG5	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 1.

Phase distribution (across all retrieved trials)

Phase	Trials
Not specified	1

Top trials by phase / activity

NCT	Phase	Status	Title
NCT05097820	Not specified	RECRUITING	Prospective Observational Study on SEBBIN Silicone Gel-filled Testicular Implants