partial chromosome Y deletion

Summary

partial chromosome Y deletion (MONDO:0015607) is a disease and 1 clinical trial. Top therapeutic interventions include alitretinoin, calcitriol, and isotretinoin. A subtype of syndrome caused by partial chromosomal deletion — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• Prevalence: 1-5 / 10 000 (Worldwide) [Orphanet-validated]
• Phenotypes (HPO): 6
• Clinical trials: 1

Clinical features

Epidemiology

Prevalence records

2 prevalence record(s), Orphanet:

Type	Class	Value	Geography	Validation
Point prevalence	1-5 / 10 000	20.8	Worldwide	Validated
Point prevalence	1-5 / 10 000	20	Europe	Validated

Signs & symptoms

Clinical features (HPO)

6 HPO clinical features (Orphanet curated; top 6 by frequency):

HPO ID	Term	Frequency
HP:0003251	Male infertility	Very frequent (80-99%)
HP:0008669	Abnormal spermatogenesis	Very frequent (80-99%)
HP:0008734	Decreased testicular size	Very frequent (80-99%)
HP:0011961	Non-obstructive azoospermia	Very frequent (80-99%)
HP:0000798	Oligozoospermia	Frequent (30-79%)
HP:0000028	Cryptorchidism	Occasional (5-29%)

Identifiers

Disease identifiers

Field	Value
Canonical name	partial chromosome Y deletion
Mondo ID	MONDO:0015607
MeSH	C536297
Orphanet	1646
SNOMED CT	717158001
UMLS	C1507149
MedGen	267211
GARD	0016574
Is cancer (heuristic)	no

Also known as: Male sterility due to chromosome Y deletion · partial deletion of chromosome Y · partial deletion of the long arm of the Y chromosome · partial deletion of Y · partial deletion of Y chromosome short arm · Y-chromosome microdeletions

Data availability: 29 cell lines.

Disease family

This is a subtype of syndrome caused by partial chromosomal deletion. Genetic, therapeutic, and trial evidence is largely curated at the broader-term level — see the parent page for the associated-gene cohort and molecular evidence.

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › chromosomal disorder › syndrome caused by partial chromosomal deletion › partial chromosome Y deletion

Related subtypes (26): Smith-Magenis syndrome, severe motor and intellectual disabilities-sensorineural deafness-dystonia syndrome, partial deletion of chromosome 1, partial deletion of chromosome 2, partial deletion of chromosome 3, partial deletion of chromosome 4, partial deletion of chromosome 5, partial deletion of chromosome 6, partial deletion of chromosome 7, partial deletion of chromosome 8, partial deletion of chromosome 9, partial deletion of chromosome 10, partial deletion of chromosome 11, partial deletion of chromosome 16, partial deletion of chromosome 17, partial deletion of chromosome 18, partial deletion of chromosome 19, partial deletion of chromosome 20, partial deletion of the long arm of chromosome 13, partial deletion of the long arm of chromosome 14, partial deletion of the long arm of chromosome 15, partial deletion of the long arm of chromosome 21, partial deletion of chromosome X, partial deletion of chromosome 12, 3q27.3 microdeletion syndrome, chromosome 22q deletion

Subtypes (3): spermatogenic failure, Y-linked, 1, spermatogenic failure, Y-linked, 2, Y chromosome infertility due to DAZ1 deletion

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

No tiered GWAS variants or ClinVar records for this disease.

Genes & proteins

No associated-gene cohort resolved for this disease. Atlas builds the molecular and therapeutic sections — associated genes, protein families, druggability, pathways, interactions, and drug associations — by aggregating over a disease’s associated genes (resolved via GWAS / GenCC / ClinVar / CIViC), and none resolved here. This is expected for antibody-mediated, autoimmune, or otherwise non-gene-defined conditions; the curated evidence for this disease is its clinical features, GWAS susceptibility, and clinical trials (above).

Function

No pathway enrichment — requires an associated-gene cohort.

Therapeutics

No druggable-target or therapeutic data for this disease’s cohort.

Clinical trials & evidence

Clinical trials

Clinical trials: 1.

Phase distribution (across all retrieved trials)

Phase	Trials
PHASE2	1

Top trials by phase / activity

NCT	Phase	Status	Title
NCT02061384	PHASE2	COMPLETED	RA-2 13-cis Retinoic Acid (Isotretinoin)

Drugs tested across these trials (top 30)

Molecule	Max phase	Trials referencing
ALITRETINOIN	4	1
CALCITRIOL	4	1
ISOTRETINOIN	4	1