SLC34A2
protein-codingsolute carrier family 34 member 2, the group of Solute carrier family 34
Gene summary
The protein encoded by this gene is a pH-sensitive sodium-dependent phosphate transporter. Phosphate uptake is increased at lower pH. Defects in this gene are a cause of pulmonary alveolar microlithiasis. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, May 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~30.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0009928
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0009928
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0009928
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0009928
Submitter: Ambry Genetics
Clinical Genomic Database (CGD)
Manifestation: Pulmonary
Intervention: Pulmonary
Rationale: Treatment with disodium editronate has been reported as effective
Comments: Individuals with cardiovascular valvular anomalies have been described
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SLC34A2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006424.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 40 | 4 | 46 | ||
| missense | 1 | 117 | 7 | 4 | 129 | |
| nonsense | 4 | 1 | 5 | |||
| start loss | 0 | |||||
| frameshift | 5 | 4 | 1 | 10 | ||
| splice donor/acceptor (+/-2bp) | 1 | 5 | 5 | 11 | ||
| Total | 10 | 10 | 126 | 47 | 8 | 201 |
Highest pathogenic variant AF is 0.000037176287
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006415.3 | 12 | MANE Select | |
| Ensembl | ENSP00000371483.3 | 12 | MANE Select | |
| RefSeq | NP_001171469.2 | 12 | Standard | |
| RefSeq | NP_001171470.2 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Mineral absorption - Homo sapiens (human)
- Vitamin D Receptor Pathway
- Surfactant metabolism
- Metabolism of proteins
- Transport of inorganic cations/anions and amino acids/oligopeptides
Biological Process
- in utero embryonic development
- phosphate ion transport
- cellular phosphate ion homeostasis
- sodium ion transmembrane transport
- response to estrogen
Molecular Function
- sodium:phosphate symporter activity
- sodium-dependent phosphate transmembrane transporter activity
- sodium ion binding
- phosphate ion binding
Cellular Component
- plasma membrane
- integral component of plasma membrane
- brush border
- integral component of membrane
- apical plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000382051
- Coding exons
- 12
- Length
- 23448
- Individuals with no LoFs
- 125631
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 117
- Defined
- 125748
- p
- 0.000465
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.145 | 391 | 399 | 0.980 | 0.0000260 | 4502 |
| Missense (PolyPhen) | 101 | 113.93 | 0.88647 | 1294 | ||
| Synonymous | -2.26 | 215 | 177 | 1.22 | 0.0000134 | 1412 |
| Loss of Function | 1.20 | 19 | 25.6 | 0.743 | 0.00000121 | 297 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00069 | 0.00069 | rare |
| Ashkenazi Jewish | 0.0019 | 0.0019 | notable |
| East Asian | 0.00076 | 0.00076 | rare |
| Finnish | 0.0011 | 0.0011 | notable |
| European (Non-Finnish) | 0.00026 | 0.00023 | rare |
| South Asian | 0.00026 | 0.00026 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be involved in actively transporting phosphate into cells via Na(+) cotransport. It may be the main phosphate transport protein in the intestinal brush border membrane. May have a role in the synthesis of surfactant in lungs' alveoli.;
- Disease
- DISEASE: Pulmonary alveolar microlithiasis (PALM) [MIM:265100]: Rare disease characterized by the deposition of calcium phosphate microliths throughout the lungs. Most patients are asymptomatic for several years or even for decades and generally, the diagnosis is incidental to clinical investigations unrelated to the disease. Cases with early-onset or rapid progression are rare. A 'sandstorm-appearing' chest roentgenogram is a typical diagnostic finding. The onset of this potentially lethal disease varies from the neonatal period to old age and the disease follows a long- term, progressive course, resulting in a slow deterioration of lung functions. Pulmonary alveolar microlithiasis is a recessive monogenic disease with full penetrance. {ECO:0000269|PubMed:16960801}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=A chromosomal aberration involving SLC34A2 is found in a glioblastoma multiforme cell line U-118MG. Results in the formation of a SLC34A2-ROS1 chimeric protein that retains a constitutive kinase activity. {ECO:0000269|PubMed:12661006}.;
Intolerance Scores
- LoFtool
- 0.299
- RVIS EVS
- 0.16
- RVIS percentile EVS
- 64.92
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.466
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |