Renal tubular acidosis, distal, 4, with hemolytic anemia

Summary

Renal tubular acidosis, distal, 4, with hemolytic anemia (MONDO:0012700) is a disease caused by SLC4A1 (GenCC Strong), with 3 cohort genes.

At a glance

• Prevalence: <1 / 1 000 000 (Europe)
• Causal gene: SLC4A1 (GenCC Strong)
• Cohort genes: 3
• ClinVar variants: 175

Clinical features

Epidemiology

Prevalence records

1 prevalence record(s), Orphanet:

Type	Class	Value	Geography	Validation
Point prevalence	<1 / 1 000 000		Europe	Not yet validated

Identifiers

Disease identifiers

Field	Value
Canonical name	renal tubular acidosis, distal, 4, with hemolytic anemia
Mondo ID	MONDO:0012700
OMIM	611590
Orphanet	93610
UMLS	C5436235
MedGen	1771439
GARD	0012354
Is cancer (heuristic)	no

Also known as: distal renal tubular acidosis 4 with hemolytic anaemia · distal renal tubular acidosis 4 with hemolytic anemia · distal renal tubular acidosis with anaemia · distal renal tubular acidosis with anemia · dRTA with anaemia · dRTA with anemia · renal tubular acidosis, distal, with hemolytic anaemia · RTA, distal, autosomal recessive, with hemolytic Anaemia

Data availability: 175 ClinVar variants · 3 GenCC gene-disease records · 1 cell line.

Disease family

Classification path: disease › human disease › disease by body system or component › hematologic disorder › anemia › normocytic anemia › hemolytic anemia › familial hemolytic anemia › renal tubular acidosis, distal, 4, with hemolytic anemia

Related subtypes (22): congenital nonspherocytic hemolytic anemia, elliptocytosis 2, southeast Asian ovalocytosis, overhydrated hereditary stomatocytosis, cryohydrocytosis, dehydrated hereditary stomatocytosis with or without pseudohyperkalemia and/or perinatal edema, abetalipoproteinemia, hemolytic anemia due to diphosphoglycerate mutase deficiency, glycogen storage disease VII, cutaneous porphyria, hereditary cryohydrocytosis with reduced stomatin, familial pseudohyperkalemia, elliptocytosis 1, glycogen storage disease due to aldolase A deficiency, primary CD59 deficiency, triosephosphate isomerase deficiency, dehydrated hereditary stomatocytosis 2, Rh deficiency syndrome, hereditary spherocytosis, congenital dyserythropoietic anemia, X-linked congenital hemolytic anemia, hemolytic disease of fetus and newborn, RH-induced

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

175 retrieved; paginated sample, class counts are floors:

107 uncertain significance, 30 conflicting classifications of pathogenicity, 12 pathogenic/likely pathogenic, 9 benign/likely benign, 7 likely benign, 6 pathogenic, 4 likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
17753	NM_000342.4(SLC4A1):c.1199_1225del (p.Ala400_Ala408del)	SLC4A1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
17762	NM_000342.3(SLC4A1):c.448C>T (p.Arg150Ter)	SLC4A1	Pathogenic	criteria provided, multiple submitters, no conflicts
17763	NM_000342.4(SLC4A1):c.1766G>A (p.Arg589His)	SLC4A1	Pathogenic	criteria provided, multiple submitters, no conflicts
17764	NM_000342.4(SLC4A1):c.1765C>T (p.Arg589Cys)	SLC4A1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
17767	NM_000342.4(SLC4A1):c.2102G>A (p.Gly701Asp)	SLC4A1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
17771	NM_000342.4(SLC4A1):c.2573C>A (p.Ala858Asp)	SLC4A1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
17772	NM_000342.4(SLC4A1):c.2545GTG[1] (p.Val850del)	SLC4A1	Pathogenic	criteria provided, single submitter
17773	NM_000342.3(SLC4A1):c.1462G>A (p.Val488Met)	SLC4A1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
17779	NM_000342.4(SLC4A1):c.1805G>C (p.Arg602Pro)	SLC4A1	Pathogenic	no assertion criteria provided
17780	NM_000342.3(SLC4A1):c.2279G>A (p.Arg760Gln)	SLC4A1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
235293	NM_000342.4(SLC4A1):c.1825G>A (p.Gly609Arg)	SLC4A1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
3382897	NM_000342.4(SLC4A1):c.2020del (p.Val674fs)	SLC4A1	Pathogenic	criteria provided, single submitter
3582115	NM_000342.4(SLC4A1):c.1242del (p.Phe414fs)	SLC4A1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
620131	NM_000342.4(SLC4A1):c.1030C>T (p.Arg344Ter)	SLC4A1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
971626	NM_000342.4(SLC4A1):c.2726T>C (p.Met909Thr)	SLC4A1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
994203	NM_000342.4(SLC4A1):c.2169G>A (p.Trp723Ter)	SLC4A1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
522609	NM_182758.4(WDR72):c.2522T>A (p.Leu841Gln)	WDR72	Pathogenic	no assertion criteria provided
522610	NM_182758.4(WDR72):c.2686C>T (p.Arg896Ter)	WDR72	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
3780627	NC_000002.12:g.42108272_42108298del		Likely pathogenic	criteria provided, single submitter
1163104	NM_000342.4(SLC4A1):c.2260C>T (p.Gln754Ter)	SLC4A1	Likely pathogenic	criteria provided, multiple submitters, no conflicts
1275803	NM_000342.4(SLC4A1):c.2716G>T (p.Glu906Ter)	SLC4A1	Likely pathogenic	criteria provided, multiple submitters, no conflicts
2433471	NM_000342.4(SLC4A1):c.349+1G>C	SLC4A1	Likely pathogenic	criteria provided, multiple submitters, no conflicts
1008971	NM_000342.4(SLC4A1):c.1181T>C (p.Leu394Pro)	SLC4A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1044950	NM_000342.4(SLC4A1):c.1160G>A (p.Arg387Gln)	SLC4A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1050262	NM_000342.4(SLC4A1):c.538C>T (p.Arg180Cys)	SLC4A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1162821	NM_000342.4(SLC4A1):c.277G>T (p.Ala93Ser)	SLC4A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1343087	NM_000342.4(SLC4A1):c.2656C>A (p.Leu886Met)	SLC4A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1343088	NM_000342.4(SLC4A1):c.713A>T (p.Glu238Val)	SLC4A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1420205	NM_000342.4(SLC4A1):c.2344C>T (p.Arg782Cys)	SLC4A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1495044	NM_000342.4(SLC4A1):c.523C>A (p.Pro175Thr)	SLC4A1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 15 · Orphanet: 9 · 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
SLC4A1	Strong	Autosomal dominant	autosomal dominant distal renal tubular acidosis	15

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
SLC4A1	Orphanet:3202	Dehydrated hereditary stomatocytosis
SLC4A1	Orphanet:398088	Hereditary cryohydrocytosis with normal stomatin
SLC4A1	Orphanet:822	Hereditary spherocytosis
SLC4A1	Orphanet:93608	Autosomal dominant distal renal tubular acidosis
SLC4A1	Orphanet:93610	Distal renal tubular acidosis with anemia
SLC4A1	Orphanet:98868	Southeast Asian ovalocytosis
WDR72	Orphanet:100033	Hypomaturation amelogenesis imperfecta
WDR72	Orphanet:402041	Autosomal recessive distal renal tubular acidosis
CCBE1	Orphanet:2136	Hennekam syndrome

Cohort genes → proteins

3 cohort genes, 3 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	3

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
SLC4A1	HGNC:11027	ENSG00000004939	P02730	Band 3 anion transport protein	gencc,clinvar
WDR72	HGNC:26790	ENSG00000166415	Q3MJ13	WD repeat-containing protein 72	clinvar
CCBE1	HGNC:29426	ENSG00000183287	Q6UXH8	Collagen and calcium-binding EGF domain-containing protein 1	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
SLC4A1	Band 3 anion transport protein	Functions both as a transporter that mediates electroneutral anion exchange across the cell membrane and as a structural protein.
WDR72	WD repeat-containing protein 72	Plays a major role in formation of tooth enamel.
CCBE1	Collagen and calcium-binding EGF domain-containing protein 1	Required for lymphangioblast budding and angiogenic sprouting from venous endothelium during embryogenesis.

Protein-family classification

Druggable: 0 · Difficult: 1 · Unknown: 2 · 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	5.8×	0.327
Other/Unknown	2	1.2×	0.587

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
SLC4A1	Other/Unknown	no		Anion_exchange, Anion_exchange_1, HCO3_transpt_euk
WDR72	Scaffold/PPI	no		WD40_rpt, WD40/YVTN_repeat-like_dom_sf, WD40_repeat_CS
CCBE1	Other/Unknown	no		EGF-type_Asp/Asn_hydroxyl_site, EGF, EGF-like_Ca-bd_dom

Expression context

Cohort genes with no expression data: 0.

3 cohort genes 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)	3
unknown	0

Top tissues across cohort

Tissue	Cohort genes
bone marrow	1
bone marrow cell	1
trabecular bone tissue	1
kidney epithelium	1
pancreatic ductal cell	1
renal medulla	1
lower lobe of lung	1
oocyte	1
secondary oocyte	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
SLC4A1	161	tissue_specific	marker	trabecular bone tissue, bone marrow, bone marrow cell
WDR72	139	tissue_specific	marker	kidney epithelium, pancreatic ductal cell, renal medulla
CCBE1	172	ubiquitous	marker	secondary oocyte, lower lobe of lung, oocyte

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
SLC4A1	1,598
WDR72	1,126
CCBE1	765

Structural data

PDB: 1 · AlphaFold-only: 2 · No structure: 0

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
SLC4A1	P02730	54

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
WDR72	Q3MJ13	67.22
CCBE1	Q6UXH8	65.61

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 11. Enrichment computed across 3 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 SLC4A1 causes hereditary spherocytosis type 4 (HSP4), distal renal tubular acidosis (dRTA) and dRTA with hemolytic anemia (dRTA-HA)	1	11420.0×	1e-03	SLC4A1
Erythrocytes take up oxygen and release carbon dioxide	1	1268.9×	0.002	SLC4A1
O2/CO2 exchange in erythrocytes	1	1268.9×	0.002	SLC4A1
Bicarbonate transporters	1	1142.0×	0.002	SLC4A1
Erythrocytes take up carbon dioxide and release oxygen	1	878.5×	0.003	SLC4A1
SLC transporter disorders	1	203.9×	0.009	SLC4A1
Disorders of transmembrane transporters	1	139.3×	0.011	SLC4A1
R-HSA-425393	1	129.8×	0.011	SLC4A1
SLC-mediated transmembrane transport	1	59.2×	0.021	SLC4A1
Transport of small molecules	1	25.1×	0.044	SLC4A1
Disease	1	13.1×	0.076	SLC4A1

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 3 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO term	Cohort genes	Fold	FDR	Sample cohort genes
response to increased oxygen levels	1	5617.3×	0.002	SLC4A1
pH elevation	1	5617.3×	0.002	SLC4A1
protein localization to plasma membrane	2	72.5×	0.002	SLC4A1, WDR72
positive regulation of lymphangiogenesis	1	1872.4×	0.003	CCBE1
lymphatic endothelial cell migration	1	1872.4×	0.003	CCBE1
intracellular monoatomic ion homeostasis	1	1404.3×	0.003	SLC4A1
negative regulation of urine volume	1	1404.3×	0.003	SLC4A1
negative regulation of glycolytic process through fructose-6-phosphate	1	936.2×	0.004	SLC4A1
venous blood vessel morphogenesis	1	802.5×	0.004	CCBE1
plasma membrane phospholipid scrambling	1	510.7×	0.005	SLC4A1
monoatomic anion transport	1	468.1×	0.005	SLC4A1
lymphangiogenesis	1	401.2×	0.005	CCBE1
positive regulation of protein processing	1	401.2×	0.005	CCBE1
positive regulation of vascular endothelial growth factor signaling pathway	1	374.5×	0.005	CCBE1
respiratory system process	1	312.1×	0.006	CCBE1
bicarbonate transport	1	267.5×	0.007	SLC4A1
biomineral tissue development	1	216.1×	0.008	WDR72
regulation of intracellular pH	1	200.6×	0.008	SLC4A1
erythrocyte development	1	175.5×	0.008	SLC4A1
positive regulation of vascular endothelial growth factor production	1	165.2×	0.008	CCBE1
sprouting angiogenesis	1	160.5×	0.008	CCBE1
chloride transport	1	151.8×	0.008	SLC4A1
positive regulation of endothelial cell migration	1	83.8×	0.014	CCBE1
chloride transmembrane transport	1	79.1×	0.015	SLC4A1
lung development	1	66.1×	0.017	CCBE1
blood coagulation	1	57.9×	0.018	SLC4A1
transmembrane transport	1	56.2×	0.018	SLC4A1
positive regulation of angiogenesis	1	38.5×	0.026	CCBE1

Therapeutics

Drug target analysis

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

Druggability breadth: 0 of 3 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
SLC4A1	0	0
WDR72	0	0
CCBE1	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Pharmacogenomics

Cohort genes with a PharmGKB record: 3; 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	3	SLC4A1, WDR72, CCBE1

Undrugged target profiles

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

Symbol	ChEMBL assays	Drugged partners (top 3)
SLC4A1	0	—
WDR72	0	—
CCBE1	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.