SLC34A2

protein-coding

solute 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

NM_006424.3

Inheritance

AR

ClinVar variants

P:20U:126B:55

Top phenotype

Pulmonary alveolar microlithiasis

gnomAD constraint

pLI —, LoF o/e 0.74

Max pathogenic AF

—

Genomic locus

chr4:25,648,011-25,678,748

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~30.7 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

pulmonary alveolar microlithiasisSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009928

Submitter: Orphanet

pulmonary alveolar microlithiasisSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009928

Submitter: Labcorp Genetics (formerly Invitae)

pulmonary alveolar microlithiasisSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009928

Submitter: PanelApp Australia

pulmonary alveolar microlithiasisDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009928

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Pulmonary alveolar microlithiasisAR

Manifestation: Pulmonary

Intervention: Pulmonary

Rationale: Treatment with disodium editronate has been reported as effective

Comments: Individuals with cardiovascular valvular anomalies have been described

Refs: 1485012; 9097354; 9258573; 11287838; 12210357; 12357485; 11956731; 12700375; 16960801; 20425862; 22336687Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC34A2 variants in ClinVar

6 Conditions Cataloged
not providedTotal: 100
Inborn genetic diseasesTotal: 92
PULMONARY ALVEOLAR MICROLITHIASISTotal: 21
SLC34A2-related disorderTotal: 19
not specifiedTotal: 11
Hereditary breast ovarian cancer syndromeTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
40
clinvar
4
clinvar
46
missense
1
clinvar
117
clinvar
7
clinvar
4
clinvar
129
nonsense
4
clinvar
1
clinvar
5
start loss
0
frameshift
5
clinvar
4
clinvar
1
clinvar
10
splice donor/acceptor (+/-2bp)
1
clinvar
5
clinvar
5
clinvar
11
Total1010126478201

Highest pathogenic variant AF is 0.000037176287

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_006424.3RefSeqNP_006415.312MANE Select
ENST00000382051.8EnsemblENSP00000371483.312MANE Select
NM_001177998.2RefSeqNP_001171469.212Standard
NM_001177999.2RefSeqNP_001171470.212Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.1453913990.9800.00002604502
Missense (PolyPhen)101113.930.886471294
Synonymous-2.262151771.220.00001341412
Loss of Function1.201925.60.7430.00000121297

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.000690.00069rare
Ashkenazi Jewish0.00190.0019notable
East Asian0.000760.00076rare
Finnish0.00110.0011notable
European (Non-Finnish)0.000260.00023rare
South Asian0.000260.00026rare
Other0.000330.00033rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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