cystinuria type A

Summary

cystinuria type A (MONDO:0019745) is a disease with 1 cohort gene.

At a glance

• Cohort genes: 1

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	cystinuria type A
Mondo ID	MONDO:0019745
MeSH	C565652
Orphanet	93612
ICD-11	1172657361
UMLS	C1857388
MedGen	347441
GARD	0016827
Is cancer (heuristic)	no

Data availability: 1 GenCC gene-disease record.

Disease family

Classification path: disease › human disease › disease by body system or component › syndromic disease › cystinuria › cystinuria type A

Related subtypes (1): cystinuria type B

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

Mendelian disease overlap and somatic drivers

GenCC: 6 · Orphanet: 4 · 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
SLC3A1	Definitive	Autosomal recessive	cystinuria	6

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
SLC3A1	Orphanet:163690	Hypotonia-cystinuria syndrome
SLC3A1	Orphanet:163693	2p21 microdeletion syndrome
SLC3A1	Orphanet:238523	Atypical hypotonia-cystinuria syndrome
SLC3A1	Orphanet:93612	Cystinuria type A

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
SLC3A1	HGNC:11025	ENSG00000138079	Q07837	Amino acid transporter heavy chain SLC3A1	gencc

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
SLC3A1	Amino acid transporter heavy chain SLC3A1	Acts as a chaperone that facilitates biogenesis and trafficking of functional transporter heteromers to the plasma membrane.

Protein-family classification

Druggable: 0 · Difficult: 0 · 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
Other/Unknown	1	1.8×	0.558

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
SLC3A1	Other/Unknown	no		GH13_cat_dom, Glyco_hydro_b, GH_hydrolase_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)	1
unknown	0

Top tissues across cohort

Tissue	Cohort genes
body of pancreas	1
gall bladder	1
metanephros cortex	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
SLC3A1	163	tissue_specific	marker	body of pancreas, gall bladder, metanephros cortex

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
SLC3A1	1,890

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
SLC3A1	Q07837	5

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 9. 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
Defective SLC3A1 causes cystinuria (CSNU)	1	5710.0×	8e-04	SLC3A1
Defective amino acid transport by SLC7A9 causes cystinuria (CSNU)	1	5710.0×	8e-04	SLC3A1
Amino acid transport across the plasma membrane	1	300.5×	0.010	SLC3A1
SLC transporter disorders	1	203.9×	0.011	SLC3A1
Disorders of transmembrane transporters	1	139.3×	0.012	SLC3A1
R-HSA-425393	1	129.8×	0.012	SLC3A1
SLC-mediated transmembrane transport	1	59.2×	0.022	SLC3A1
Transport of small molecules	1	25.1×	0.045	SLC3A1
Disease	1	13.1×	0.076	SLC3A1

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
basic amino acid transport	1	16852.0×	4e-04	SLC3A1
L-cystine transport	1	2808.7×	0.001	SLC3A1
aspartate transmembrane transport	1	1404.3×	0.002	SLC3A1
L-glutamate transmembrane transport	1	802.5×	0.002	SLC3A1
amino acid transport	1	312.1×	0.004	SLC3A1
carbohydrate metabolic process	1	135.9×	0.009	SLC3A1
gene expression	1	79.9×	0.013	SLC3A1

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
SLC3A1	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	0
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	1	SLC3A1

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)
SLC3A1	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.