Nephronophthisis-like nephropathy 2

disease

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Summary

Nephronophthisis-like nephropathy 2 (MONDO:0859175) is a disease with 1 cohort gene.

At a glance

Cohort genes: 1
ClinVar variants: 4

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	nephronophthisis-like nephropathy 2
Mondo ID	MONDO:0859175
OMIM	619468
UMLS	C5561953
MedGen	1794163
GARD	0026664
Is cancer (heuristic)	no

Data availability: 4 ClinVar variants · 2 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary disease › autosomal genetic disease › autosomal recessive disease › nephronophthisis › nephronophthisis-like nephropathy 2

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

4 retrieved; paginated sample, class counts are floors:

1 pathogenic, 1 benign/likely benign, 1 likely benign, 1 uncertain significance

ClinVar	Variant (HGVS)	Gene	Classification	Review
1192530	NM_173854.6(SLC41A1):c.698G>T (p.Gly233Val)	SLC41A1	Pathogenic	no assertion criteria provided
3391046	NM_173854.6(SLC41A1):c.1277C>T (p.Thr426Ile)	SLC41A1	Uncertain significance	criteria provided, single submitter
1578086	NM_173854.6(SLC41A1):c.1161A>G (p.Gln387=)	SLC41A1	Benign/Likely benign	criteria provided, multiple submitters, no conflicts
1598449	NM_173854.6(SLC41A1):c.993-4A>G	SLC41A1	Likely benign	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 3 · Orphanet: 0 · 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
SLC41A1	Limited	Unknown	nephronophthisis-like nephropathy 2	3

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
SLC41A1	HGNC:19429	ENSG00000133065	Q8IVJ1	Solute carrier family 41 member 1	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
SLC41A1	Solute carrier family 41 member 1	Na(+)/Mg(2+) ion exchanger that acts as a predominant Mg(2+) efflux system at 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)
SLC41A1	Other/Unknown	no		SLC41_membr_dom, SLC41_membr_dom_sf, SLC41A1-3

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
cardiac muscle of right atrium	1
left ventricle myocardium	1
myocardium	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
SLC41A1	241	ubiquitous	marker	left ventricle myocardium, cardiac muscle of right atrium, myocardium

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
SLC41A1	1,033

Structural data

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

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
SLC41A1	Q8IVJ1	78.41

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 4. 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
Metal ion SLC transporters	1	601.0×	0.007	SLC41A1
R-HSA-425366	1	181.3×	0.011	SLC41A1
SLC-mediated transmembrane transport	1	59.2×	0.023	SLC41A1
Transport of small molecules	1	25.1×	0.040	SLC41A1

GO biological processes by enrichment

GO term	Cohort genes	Fold	FDR	Sample cohort genes
magnesium ion transmembrane transport	1	4213.0×	7e-04	SLC41A1
intracellular magnesium ion homeostasis	1	2808.7×	7e-04	SLC41A1
cellular response to magnesium ion	1	2407.4×	7e-04	SLC41A1
metal ion transport	1	1872.4×	7e-04	SLC41A1
magnesium ion transport	1	1203.7×	8e-04	SLC41A1

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
SLC41A1	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	SLC41A1

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)
SLC41A1	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.

Cohort genes: SLC41A1