Breasts and/or nipples, aplasia or hypoplasia of, 2

Summary

Breasts and/or nipples, aplasia or hypoplasia of, 2 (MONDO:0014450) is a disease caused by PTPRF (GenCC Strong), with 1 cohort gene.

At a glance

• Causal gene: PTPRF (GenCC Strong)
• Cohort genes: 1
• ClinVar variants: 3

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	breasts and/or nipples, aplasia or hypoplasia of, 2
Mondo ID	MONDO:0014450
OMIM	616001
UMLS	C4014918
MedGen	863355
GARD	0016044
Is cancer (heuristic)	no

Also known as: BNAH2 · breasts and/or nipples, aplasia or hypoplasia of, 2 · breasts and/or nipples, aplasia or hypoplasia of, type 2 · isolated congenital breast hypoplasia/aplasia caused by mutation in PTPRF · PTPRF isolated congenital breast hypoplasia/aplasia

Data availability: 3 ClinVar variants · 2 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by body system or component › breast disorder › isolated congenital breast hypoplasia/aplasia › breasts and/or nipples, aplasia or hypoplasia of, 2

Related subtypes (2): amastia, breasts and/or nipples, aplasia or hypoplasia of, 1

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 pathogenic, 1 likely pathogenic, 1 uncertain significance

ClinVar	Variant (HGVS)	Gene	Classification	Review
155912	NM_002840.5(PTPRF):c.1847_1848del (p.Val616fs)	PTPRF	Pathogenic	no assertion criteria provided
4845793	NM_002840.5(PTPRF):c.959del (p.Lys320fs)	PTPRF	Likely pathogenic	criteria provided, single submitter
801472	NM_002840.5(PTPRF):c.5190C>A (p.His1730Gln)	PTPRF	Uncertain significance	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 2 · 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
PTPRF	Strong	Autosomal recessive	breasts and/or nipples, aplasia or hypoplasia of, 2	2

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
PTPRF	Orphanet:180188	Isolated congenital breast hypoplasia/aplasia

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
PTPRF	HGNC:9670	ENSG00000142949	P10586	Receptor-type tyrosine-protein phosphatase F	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
PTPRF	Receptor-type tyrosine-protein phosphatase F	Possible cell adhesion receptor.

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
Phosphatase	1	83.9×	0.012

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
PTPRF	Phosphatase	yes	3.1.3.48	PTP_cat, Tyr_Pase_dom, Tyr_Pase_cat

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
bronchial epithelial cell	1
gingival epithelium	1
nipple	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
PTPRF	283	ubiquitous	marker	gingival epithelium, bronchial epithelial cell, nipple

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
PTPRF	2,473

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
PTPRF	P10586	13

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 3. 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
Receptor-type tyrosine-protein phosphatases	1	571.0×	0.003	PTPRF
Synaptic adhesion-like molecules	1	543.8×	0.003	PTPRF
Insulin receptor recycling	1	380.7×	0.003	PTPRF

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
negative regulation of receptor binding	1	16852.0×	6e-04	PTPRF
neuron projection regeneration	1	4213.0×	0.001	PTPRF
regulation of axon regeneration	1	2407.4×	0.001	PTPRF
cell surface receptor protein tyrosine phosphatase signaling pathway	1	2106.5×	0.001	PTPRF
peptidyl-tyrosine dephosphorylation	1	887.0×	0.002	PTPRF
synaptic membrane adhesion	1	581.1×	0.003	PTPRF
cell migration	1	61.5×	0.023	PTPRF
nervous system development	1	45.9×	0.027	PTPRF
cell adhesion	1	37.5×	0.030	PTPRF
signal transduction	1	16.1×	0.062	PTPRF

Therapeutics

Drug target analysis

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

Druggability breadth: 1 of 1 evidence-associated genes (100%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
PTPRF	1	2

Drugs targeting cohort genes (top 30)

Molecule	Max phase	Targets in cohort
URSOLIC ACID	2	PTPRF

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

Symbol	Assays	Type breakdown
PTPRF	136	Binding:135, Functional:1

Cohort enzymes (BRENDA EC)

Symbol	EC numbers	Names
PTPRF	3.1.3.48	protein-tyrosine-phosphatase

Cohort genes with high screening signal

≥100 ChEMBL assays — a studied-ness signal; see Therapeutics for approved-drug status.

Symbol	ChEMBL assays
PTPRF	136

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

1 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.

Compound	Max phase	Cohort target (bioactivity)
URSOLIC ACID	2	PTPRF

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	1	PTPRF
C	Druggable family + PDB, no drug	0
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	0

Undrugged target profiles

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

Clinical trials & evidence

Clinical trials

Clinical trials: 0.