SLC24A4
Basic information
Region (hg38): 14:92322581-92501481
Links
Phenotypes
GenCC
Source:
- amelogenesis imperfecta hypomaturation type 2A5 (Strong), mode of inheritance: AR
- amelogenesis imperfecta, type 3A (Supportive), mode of inheritance: AD
- amelogenesis imperfecta type 2 (Supportive), mode of inheritance: AR
- amelogenesis imperfecta hypomaturation type 2A5 (Moderate), mode of inheritance: AR
- amelogenesis imperfecta hypomaturation type 2A5 (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Ameliogenesis imperfecta, hypomaturation type, IIA5 | 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 | Dental | 23375655; 24621671 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (92 variants)
- not_provided (30 variants)
- SLC24A4-related_disorder (13 variants)
- Amelogenesis_imperfecta_hypomaturation_type_2A5 (5 variants)
- Amelogenesis_imperfecta (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC24A4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000153646.4. 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 | 17 | 24 | ||||
missense | 88 | 102 | ||||
nonsense | 3 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 5 | 0 | 88 | 25 | 11 |
Highest pathogenic variant AF is 0.000005476601
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SLC24A4 | protein_coding | protein_coding | ENST00000532405 | 17 | 173672 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.20e-11 | 0.962 | 125697 | 0 | 51 | 125748 | 0.000203 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.805 | 340 | 384 | 0.884 | 0.0000229 | 4060 |
Missense in Polyphen | 98 | 135.52 | 0.72315 | 1460 | ||
Synonymous | -0.0619 | 165 | 164 | 1.01 | 0.0000115 | 1234 |
Loss of Function | 2.19 | 23 | 37.5 | 0.614 | 0.00000213 | 366 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000479 | 0.000479 |
Ashkenazi Jewish | 0.0000993 | 0.0000992 |
East Asian | 0.000109 | 0.000109 |
Finnish | 0.000139 | 0.000139 |
European (Non-Finnish) | 0.000216 | 0.000211 |
Middle Eastern | 0.000109 | 0.000109 |
South Asian | 0.000262 | 0.000261 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Transports 1 Ca(2+) and 1 K(+) in exchange for 4 Na(+). Controls the rapid response termination and proper regulation of adaptation in olfactory sensory neurons (OSNs) which subsequently influences how odor information is encoded and perceived. May play a role in calcium transport during amelogenesis (By similarity). {ECO:0000250|UniProtKB:Q8CGQ8}.;
- Disease
- DISEASE: Amelogenesis imperfecta, hypomaturation type, 2A5 (AI2A5) [MIM:615887]: A defect of enamel formation. The disorder involves both primary and secondary dentitions. The teeth have a shiny agar jelly appearance and the enamel is softer than normal. Brown pigment is present in middle layers of enamel. {ECO:0000269|PubMed:23375655, ECO:0000269|PubMed:24621671}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Olfactory transduction - Homo sapiens (human);Sodium/Calcium exchangers;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules
(Consensus)
Recessive Scores
- pRec
- 0.150
Intolerance Scores
- loftool
- 0.871
- rvis_EVS
- 0.32
- rvis_percentile_EVS
- 72.8
Haploinsufficiency Scores
- pHI
- 0.155
- hipred
- Y
- hipred_score
- 0.538
- ghis
- 0.500
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.197
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc24a4
- Phenotype
- growth/size/body region phenotype; taste/olfaction phenotype; endocrine/exocrine gland phenotype; craniofacial phenotype; homeostasis/metabolism phenotype; skeleton phenotype; hematopoietic system 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype;
Gene ontology
- Biological process
- ion transport;potassium ion transport;cellular calcium ion homeostasis;sensory perception of smell;sodium ion transmembrane transport;response to stimulus;calcium ion transmembrane transport;amelogenesis
- Cellular component
- cytoplasm;plasma membrane;integral component of plasma membrane;membrane
- Molecular function
- calcium channel activity;calcium, potassium:sodium antiporter activity;symporter activity