GeneBe

ALX3

ALX homeobox 3, the group of PRD class homeoboxes and pseudogenes

Basic information

Region (hg38): 1:110059870-110070672

Previous symbols: [ "FND" ]

Links

ENSG00000156150 ∙ NCBI:257 ∙ OMIM:606014 ∙ HGNC:449 ∙ Uniprot:O95076 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • frontorhiny (Definitive), mode of inheritance: AR
  • frontorhiny (Strong), mode of inheritance: AR
  • frontorhiny (Supportive), mode of inheritance: AR
  • frontorhiny (Strong), mode of inheritance: AR
  • frontorhiny (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Frontonasal dysplasia 1ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Musculoskeletal; Neurologic17963218; 19409524; 22106187

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ALX3 gene.

  • Inborn_genetic_diseases (55 variants)
  • not_provided (21 variants)
  • Frontorhiny (11 variants)
  • ALX3-related_disorder (3 variants)
  • not_specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALX3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006492.3. 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
7
clinvar
3
clinvar
 10
missense
3
clinvar
57
clinvar
3
clinvar
 63
nonsense
4
clinvar
 4
start loss
0
frameshift
1
clinvar
1
clinvar
 2
splice donor/acceptor (+/-2bp)
1
clinvar
 1
Total 9 1 57 10 3

Highest pathogenic variant AF is 0.0000037174

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ALX3protein_codingprotein_codingENST00000369792 410707
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.01910.907125740071257470.0000278
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4461511670.9030.00001032178
Missense in Polyphen5478.3960.68881805
Synonymous0.4756368.00.9270.00000385752
Loss of Function1.5148.870.4514.64e-7122

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00009050.0000905
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004620.0000462
European (Non-Finnish)0.00003550.0000352
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Transcriptional regulator with a possible role in patterning of mesoderm during development. {ECO:0000250}.;
Disease
DISEASE: Frontonasal dysplasia 1 (FND1) [MIM:136760]: The term frontonasal dysplasia describes an array of abnormalities affecting the eyes, forehead and nose and linked to midfacial dysraphia. The clinical picture is highly variable. Major findings include true ocular hypertelorism; broadening of the nasal root; median facial cleft affecting the nose and/or upper lip and palate; unilateral or bilateral clefting of the alae nasi; lack of formation of the nasal tip; anterior cranium bifidum occultum; a V-shaped or widow's peak frontal hairline. {ECO:0000269|PubMed:19409524}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.0999

Intolerance Scores

loftool
0.150
rvis_EVS
-0.25
rvis_percentile_EVS
35.75

Haploinsufficiency Scores

pHI
0.521
hipred
N
hipred_score
0.410
ghis
0.626

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.467

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Alx3
Phenotype
craniofacial phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region 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); reproductive system phenotype; vision/eye phenotype; digestive/alimentary phenotype; 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); limbs/digits/tail phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; embryo phenotype;

Gene ontology

Biological process
regulation of transcription by RNA polymerase II;pattern specification process;embryonic forelimb morphogenesis;embryonic hindlimb morphogenesis;regulation of apoptotic process;embryonic cranial skeleton morphogenesis
Cellular component
nucleus
Molecular function
RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding