RAX2

retina and anterior neural fold homeobox 2, the group of PRD class homeoboxes and pseudogenes

Basic information

Region (hg38): 19:3769089-3772228

Previous symbols: [ "RAXL1" ]

Links

ENSG00000173976 ∙ NCBI:84839 ∙ OMIM:610362 ∙ HGNC:18286 ∙ Uniprot:Q96IS3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• retinitis pigmentosa (Moderate), mode of inheritance: AR
• cone-rod dystrophy (Supportive), mode of inheritance: AD
• retinitis pigmentosa 95 (Limited), mode of inheritance: AR
• cone-rod dystrophy 11 (Strong), mode of inheritance: AD
• cone-rod dystrophy 11 (Strong), mode of inheritance: AD
• retinitis pigmentosa 95 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cone-rod dystrophy 11; Retinitis pigmentosa 95	AD/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	Ophthalmologic	15028672; 30377383

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RAX2 gene.

• Cone-rod dystrophy 11 (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAX2 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				54	2	56
missense		1	100	2	1	104
nonsense			2			2
start loss						0
frameshift	1		6			7
inframe indel			2	1		3
splice donor/acceptor (+/-2bp)	1					1
splice region			2	3	1	6
non coding			31	19	15	65
Total	2	1	141	76	18

Variants in RAX2

This is a list of pathogenic ClinVar variants found in the RAX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-3769098-A-G		Cone-rod dystrophy 11 • Age related macular degeneration 6	Uncertain significance (Jan 12, 2018)
19-3769131-T-C		Age related macular degeneration 6 • Cone-rod dystrophy 11	Uncertain significance (Jan 12, 2018)
19-3769138-G-A		Age related macular degeneration 6 • Cone-rod dystrophy 11	Uncertain significance (Jan 13, 2018)
19-3769255-G-C		Cone-rod dystrophy 11 • Age related macular degeneration 6	Benign (Jan 12, 2018)
19-3769297-T-C		Cone-rod dystrophy 11 • Age related macular degeneration 6	Benign (Jan 13, 2018)
19-3769416-C-T		Macular degeneration • Cone-Rod Dystrophy, Dominant	Uncertain significance (Jun 14, 2016)
19-3769452-C-T		Age related macular degeneration 6 • Cone-rod dystrophy 11	Benign/Likely benign (Jan 12, 2018)
19-3769472-G-A		Cone-rod dystrophy 11 • Age related macular degeneration 6	Benign (Jan 13, 2018)
19-3769476-C-T		Cone-Rod Dystrophy, Dominant • Macular degeneration	Uncertain significance (Jun 14, 2016)
19-3769528-GGTGATCTGGGA-G		Cone-Rod Dystrophy, Dominant • Macular degeneration	Likely benign (Jun 14, 2016)
19-3769567-G-A		Age related macular degeneration 6 • Cone-rod dystrophy 11	Benign/Likely benign (Jan 12, 2018)
19-3769649-A-T		Cone-rod dystrophy 11 • Age related macular degeneration 6	Uncertain significance (Jan 12, 2018)
19-3769672-G-A		Age related macular degeneration 6 • Cone-rod dystrophy 11	Uncertain significance (Jan 12, 2018)
19-3769703-C-T		Cone-rod dystrophy 11 • Age related macular degeneration 6	Uncertain significance (Jan 12, 2018)
19-3769719-C-A		Age related macular degeneration 6 • Cone-rod dystrophy 11	Benign (Jan 13, 2018)
19-3769724-G-A		Cone-rod dystrophy 11 • Age related macular degeneration 6	Uncertain significance (Jan 13, 2018)
19-3769755-G-A		Cone-rod dystrophy 11 • Age related macular degeneration 6	Benign (Jan 13, 2018)
19-3769836-C-T		Cone-rod dystrophy 11 • Age related macular degeneration 6	Benign (Jan 13, 2018)
19-3769837-G-A		Cone-rod dystrophy 11 • Age related macular degeneration 6	Uncertain significance (Jan 13, 2018)
19-3769845-G-A		Age related macular degeneration 6 • Cone-rod dystrophy 11	Uncertain significance (Jan 13, 2018)
19-3769870-C-T		Age related macular degeneration 6 • Cone-rod dystrophy 11	Uncertain significance (Jan 13, 2018)
19-3769896-CCTGG-C		Macular degeneration • Cone-Rod Dystrophy, Dominant	Benign (Jun 14, 2016)
19-3769901-C-T		Age related macular degeneration 6 • Cone-rod dystrophy 11	Benign (Jan 13, 2018)
19-3769932-G-A		Cone-rod dystrophy 11 • Age related macular degeneration 6	Benign (Jan 12, 2018)
19-3769934-T-C		Cone-rod dystrophy 11 • Age related macular degeneration 6	Uncertain significance (Mar 23, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAX2	protein_coding	protein_coding	ENST00000555633	2	3147

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00829	0.581	108910	0	3	108913	0.0000138

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.169	118	123	0.957	0.00000905	1126
Missense in Polyphen		53	56.919	0.93115		528
Synonymous	0.877	50	58.5	0.854	0.00000436	421
Loss of Function	0.208	3	3.41	0.879	1.47e-7	38

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000667	0.0000667
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000107	0.0000104
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in modulating the expression of photoreceptor specific genes. Binds to the Ret-1 and Bat-1 element within the rhodopsin promoter. {ECO:0000269|PubMed:15028672}.
• Disease: DISEASE: Macular degeneration, age-related, 6 (ARMD6) [MIM:613757]: A form of age-related macular degeneration, a multifactorial eye disease and the most common cause of irreversible vision loss in the developed world. In most patients, the disease is manifest as ophthalmoscopically visible yellowish accumulations of protein and lipid that lie beneath the retinal pigment epithelium and within an elastin-containing structure known as Bruch membrane. {ECO:0000269|PubMed:15028672}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Cone-rod dystrophy 11 (CORD11) [MIM:610381]: An inherited retinal dystrophy characterized by retinal pigment deposits visible on fundus examination, predominantly in the macular region, and initial loss of cone photoreceptors followed by rod degeneration. This leads to decreased visual acuity and sensitivity in the central visual field, followed by loss of peripheral vision. Severe loss of vision occurs earlier than in retinitis pigmentosa, due to cone photoreceptors degenerating at a higher rate than rod photoreceptors. {ECO:0000269|PubMed:15028672}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.175

Haploinsufficiency Scores

• pHI: 0.209
• hipred: N
• hipred_score: 0.215
• ghis: 0.465

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.228

Gene Damage Prediction

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

Gene ontology

• Biological process: visual perception;positive regulation of transcription by RNA polymerase II;response to stimulus
• 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