RAX

retina and anterior neural fold homeobox, the group of PRD class homeoboxes and pseudogenes

Basic information

Region (hg38): 18:59267034-59274086

Links

ENSG00000134438 ∙ NCBI:30062 ∙ OMIM:601881 ∙ HGNC:18662 ∙ Uniprot:Q9Y2V3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• isolated microphthalmia 3 (Definitive), mode of inheritance: AR
• isolated microphthalmia 3 (Strong), mode of inheritance: AR
• isolated anophthalmia-microphthalmia syndrome (Supportive), mode of inheritance: AD
• isolated microphthalmia 3 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Microphthalmia, syndromic 16	AR	Endocrine	The condition has been described as including panhypopituitarism in some individuals, and awareness may allow early diagnosis and medical management of endocrine manifestations	Craniofacial; Endocrine; Ophthalmologic	14662654; 18783408; 22736936; 24033328; 28831107; 30811539

ClinVar

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

• Isolated microphthalmia 3 (95 variants)
• not provided (37 variants)
• Inborn genetic diseases (23 variants)
• Anophthalmia-microphthalmia syndrome (5 variants)
• not specified (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAX gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			5	14	1	20
missense			43	1	2	46
nonsense	1	1				2
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3		3
non coding			40	18	9	67
Total	1	2	88	33	12

Variants in RAX

This is a list of pathogenic ClinVar variants found in the RAX region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
18-59267083-G-A		Isolated microphthalmia 3	Uncertain significance (Jan 13, 2018)
18-59267126-A-G		Isolated microphthalmia 3	Likely benign (Apr 27, 2017)
18-59267187-T-C		Isolated microphthalmia 3	Uncertain significance (Jan 13, 2018)
18-59267209-G-A		Isolated microphthalmia 3	Uncertain significance (Jan 13, 2018)
18-59267233-C-T		Isolated microphthalmia 3	Uncertain significance (Jan 12, 2018)
18-59267248-G-T		Isolated microphthalmia 3	Uncertain significance (Jan 13, 2018)
18-59267258-C-T		Isolated microphthalmia 3	Benign (Jan 13, 2018)
18-59267267-G-T		Isolated microphthalmia 3	Uncertain significance (Jan 13, 2018)
18-59267330-T-C		Isolated microphthalmia 3	Uncertain significance (Mar 16, 2018)
18-59267353-C-T		Isolated microphthalmia 3	Uncertain significance (Apr 27, 2017)
18-59267440-A-G		Isolated microphthalmia 3	Benign (Apr 27, 2017)
18-59267457-C-A		Isolated microphthalmia 3	Uncertain significance (Jan 12, 2018)
18-59267479-C-T		Isolated microphthalmia 3	Uncertain significance (Jan 13, 2018)
18-59267488-C-G		Isolated microphthalmia 3	Likely benign (Jan 13, 2018)
18-59267567-C-A		Isolated microphthalmia 3	Uncertain significance (Jan 12, 2018)
18-59267567-C-T		Isolated microphthalmia 3	Likely benign (Jan 13, 2018)
18-59267586-C-T		Isolated microphthalmia 3	Uncertain significance (Jan 13, 2018)
18-59267615-G-C		Isolated microphthalmia 3	Uncertain significance (Jan 12, 2018)
18-59267629-ACG-A		Anophthalmia-microphthalmia syndrome	Uncertain significance (Jun 14, 2016)
18-59267630-CG-C		Anophthalmia-microphthalmia syndrome	Uncertain significance (Jun 14, 2016)
18-59267631-GC-G		Anophthalmia-microphthalmia syndrome	Uncertain significance (Jun 14, 2016)
18-59267631-GCC-G		Anophthalmia-microphthalmia syndrome	Likely benign (Jun 14, 2016)
18-59267639-C-A		Isolated microphthalmia 3	Uncertain significance (Jan 12, 2018)
18-59267641-C-A		Isolated microphthalmia 3	Uncertain significance (Jan 13, 2018)
18-59267642-C-G		Isolated microphthalmia 3	Uncertain significance (Jan 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAX	protein_coding	protein_coding	ENST00000334889	3	7052

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.101	0.869	125727	0	6	125733	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.189	168	175	0.960	0.00000825	2124
Missense in Polyphen		50	63.257	0.79042		727
Synonymous	-0.147	90	88.2	1.02	0.00000423	783
Loss of Function	1.86	3	9.02	0.333	3.93e-7	103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000186	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a critical role in eye formation by regulating the initial specification of retinal cells and/or their subsequent proliferation. Binds to the photoreceptor conserved element-I (PCE-1/Ret 1) in the photoreceptor cell-specific arrestin promoter.

Recessive Scores

• pRec: 0.110

Haploinsufficiency Scores

• pHI: 0.250
• hipred: Y
• hipred_score: 0.718
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.673

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rax
• Phenotype: growth/size/body region phenotype; craniofacial phenotype; cellular phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); normal 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); vision/eye phenotype

Zebrafish Information Network

• Gene name: rx3
• Affected structure: ethmoid cartilage
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: pattern specification process;visual perception;hypothalamus development;camera-type eye development;positive regulation of transcription by RNA polymerase II;limb development
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific