GeneBe

SLC24A4

solute carrier family 24 member 4, the group of Solute carrier family 24

Basic information

Region (hg38): 14:92322581-92501481

Links

ENSG00000140090 ∙ NCBI:123041 ∙ OMIM:609840 ∙ HGNC:10978 ∙ Uniprot:Q8NFF2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Ameliogenesis imperfecta, hypomaturation type, IIA5ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingDental23375655; 24621671

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC24A4 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
17
clinvar
7
clinvar
 24
missense
2
clinvar
88
clinvar
8
clinvar
4
clinvar
 102
nonsense
3
clinvar
 3
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 5 0 88 25 11

Highest pathogenic variant AF is 0.000005476601

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SLC24A4protein_codingprotein_codingENST00000532405 17173672
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
2.20e-110.9621256970511257480.000203
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.8053403840.8840.00002294060
Missense in Polyphen98135.520.723151460
Synonymous-0.06191651641.010.00001151234
Loss of Function2.192337.50.6140.00000213366

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004790.000479
Ashkenazi Jewish0.00009930.0000992
East Asian0.0001090.000109
Finnish0.0001390.000139
European (Non-Finnish)0.0002160.000211
Middle Eastern0.0001090.000109
South Asian0.0002620.000261
Other0.0001630.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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