SLC26A2
solute carrier family 26 member 2, the group of Solute carrier family 26
Basic information
Region (hg38): 5:149960758-149993455
Previous symbols: [ "DTD" ]
Links
Phenotypes
GenCC
Source:
- achondrogenesis type IB (Definitive), mode of inheritance: AR
- multiple epiphyseal dysplasia type 4 (Definitive), mode of inheritance: AR
- multiple epiphyseal dysplasia type 4 (Moderate), mode of inheritance: AR
- diastrophic dysplasia (Strong), mode of inheritance: AR
- atelosteogenesis type II (Moderate), mode of inheritance: AR
- achondrogenesis type IB (Moderate), mode of inheritance: AR
- diastrophic dysplasia (Supportive), mode of inheritance: AR
- atelosteogenesis type II (Supportive), mode of inheritance: AR
- achondrogenesis type IB (Supportive), mode of inheritance: AR
- multiple epiphyseal dysplasia type 4 (Supportive), mode of inheritance: AR
- diastrophic dysplasia (Strong), mode of inheritance: AR
- diastrophic dysplasia (Definitive), mode of inheritance: AR
- achondrogenesis type IB (Definitive), mode of inheritance: AR
- multiple epiphyseal dysplasia (Definitive), mode of inheritance: AR
- atelosteogenesis type II (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Achondrogenesis, type IB; Atelosteogenesis II; De la Chapelle dysplasia; Diastrophic dysplasia; Epiphyseal dysplasia, multiple, 4 | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Musculoskeletal | 13993535; 5703690; 3799721; 4644462; 4064368; 3562108; 8528239; 8571951; 8723083; 8931695; 8723100; 1345170; 7923357; 9108864; 10482955; 10466420; 10465113; 11734236; 11565064; 11303514; 12525546; 12966518; 12220459; 15316973; 18708426; 18925670; 20301483; 20301689; 20525296; 21077202; 21155763; 21922596; 22052783 |
ClinVar
This is a list of variants' phenotypes submitted to
- Achondrogenesis,_type_IB (668 variants)
- Multiple_epiphyseal_dysplasia_type_4 (630 variants)
- Diastrophic_dysplasia (627 variants)
- Atelosteogenesis_type_II (607 variants)
- not_provided (73 variants)
- Inborn_genetic_diseases (70 variants)
- Sulfate_transporter-related_osteochondrodysplasia (49 variants)
- not_specified (23 variants)
- Connective_tissue_disorder (14 variants)
- SLC26A2-related_disorder (9 variants)
- Osteochondrodysplasia (8 variants)
- 3MC_syndrome_2 (4 variants)
- SLC26A2-related_skeletal_dysplasia (2 variants)
- Diastrophic_dysplasia,_broad_bone-platyspondylic_variant (1 variants)
- De_la_Chapelle_dysplasia (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC26A2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000112.4. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 13 | 265 | 279 | |||
| missense | 31 | 230 | 18 | 287 | ||
| nonsense | 19 | 33 | 52 | |||
| start loss | 1 | 1 | ||||
| frameshift | 52 | 84 | 138 | |||
| splice donor/acceptor (+/-2bp) | 5 | |||||
| Total | 80 | 152 | 245 | 283 | 2 |
Highest pathogenic variant AF is 0.00142002
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLC26A2 | protein_coding | protein_coding | ENST00000286298 | 2 | 32719 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 7.50e-7 | 0.735 | 125692 | 0 | 53 | 125745 | 0.000211 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0314 | 370 | 372 | 0.995 | 0.0000184 | 4837 |
| Missense in Polyphen | 147 | 141.64 | 1.0378 | 1857 | ||
| Synonymous | 0.419 | 130 | 136 | 0.954 | 0.00000657 | 1509 |
| Loss of Function | 1.23 | 12 | 17.6 | 0.683 | 8.48e-7 | 272 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000483 | 0.000478 |
| Ashkenazi Jewish | 0.0000993 | 0.0000992 |
| East Asian | 0.000217 | 0.000217 |
| Finnish | 0.0000924 | 0.0000924 |
| European (Non-Finnish) | 0.000203 | 0.000202 |
| Middle Eastern | 0.000217 | 0.000217 |
| South Asian | 0.000327 | 0.000327 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Sulfate transporter. May play a role in endochondral bone formation. {ECO:0000269|PubMed:7923357}.;
- Disease
- DISEASE: Achondrogenesis 1B (ACG1B) [MIM:600972]: A form of achondrogenesis type 1, a lethal form of chondrodysplasia characterized by deficient ossification in the lumbar vertebrae and absent ossification in the sacral, pubic and ischial bones and clinically by stillbirth or early death. In addition to severe micromelia, there is a disproportionately large cranium due to marked edema of soft tissues. ACG1B is an autosomal recessive disease. {ECO:0000269|PubMed:8528239}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Atelosteogenesis 2 (AO2) [MIM:256050]: A perinatal dysplasia characterized by shortening of the limbs, a dysmorphic syndrome and radiographic skeletal features. Patients are stillborn or die soon after birth. {ECO:0000269|PubMed:8571951}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Multiple epiphyseal dysplasia 4 (EDM4) [MIM:226900]: A generalized skeletal dysplasia associated with significant morbidity. Joint pain, joint deformity, waddling gait, and short stature are the main clinical signs and symptoms. Radiological examination of the skeleton shows delayed, irregular mineralization of the epiphyseal ossification centers and of the centers of the carpal and tarsal bones. Multiple epiphyseal dysplasia is broadly categorized into the more severe Fairbank and the milder Ribbing types. The Fairbank type is characterized by shortness of stature, short and stubby fingers, small epiphyses in several joints, including the knee, ankle, hand, and hip. The Ribbing type is confined predominantly to the hip joints and is characterized by hands that are normal and stature that is normal or near-normal. Multiple epiphyseal dysplasia type 4 is a recessively inherited form, characterized by early childhood-onset hip dysplasia and recurrent patella dislocation. Short stature is not frequent. {ECO:0000269|PubMed:12966518, ECO:0000269|PubMed:21922596}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Transport and synthesis of PAPS;Metabolism of carbohydrates;Phase II - Conjugation of compounds;Glycosaminoglycan metabolism;Biological oxidations;Metabolism;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Cytosolic sulfonation of small molecules;Methionine and cysteine metabolism;Multifunctional anion exchangers
(Consensus)
Recessive Scores
- pRec
- 0.194
Intolerance Scores
- loftool
- 0.202
- rvis_EVS
- 0.18
- rvis_percentile_EVS
- 66.17
Haploinsufficiency Scores
- pHI
- 0.0942
- hipred
- N
- hipred_score
- 0.197
- ghis
- 0.374
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.152
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc26a2
- Phenotype
- growth/size/body region phenotype; cellular phenotype; craniofacial phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); skeleton phenotype; limbs/digits/tail phenotype;
Zebrafish Information Network
- Gene name
- slc26a2
- Affected structure
- neuromast hair cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- ossification;ion transport;bicarbonate transport;oxalate transport;3'-phosphoadenosine 5'-phosphosulfate biosynthetic process;sulfate transmembrane transport;chloride transmembrane transport
- Cellular component
- plasma membrane;integral component of plasma membrane;membrane;apical plasma membrane;microvillus membrane;extracellular exosome
- Molecular function
- secondary active sulfate transmembrane transporter activity;bicarbonate transmembrane transporter activity;chloride transmembrane transporter activity;sulfate transmembrane transporter activity;anion:anion antiporter activity;oxalate transmembrane transporter activity