RAI2

retinoic acid induced 2

Basic information

Region (hg38): X:17800049-17861337

Links

ENSG00000131831 ∙ NCBI:10742 ∙ OMIM:300217 ∙ HGNC:9835 ∙ Uniprot:Q9Y5P3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RAI2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAI2 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				4	4	8
missense			32	1	1	34
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	6	5

Variants in RAI2

This is a list of pathogenic ClinVar variants found in the RAI2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-17800429-G-A		not specified	Uncertain significance (Aug 10, 2021)
X-17800489-C-T		not specified	Uncertain significance (Jun 24, 2022)
X-17800581-C-T		not specified	Uncertain significance (Mar 07, 2024)
X-17800583-C-A		not specified	Uncertain significance (Mar 17, 2023)
X-17800591-C-G		not specified	Uncertain significance (Jan 31, 2024)
X-17800602-C-G		not specified	Uncertain significance (Aug 04, 2023)
X-17800625-G-A			Likely benign (Apr 16, 2018)
X-17800632-C-T		not specified	Uncertain significance (Jun 17, 2024)
X-17800657-A-G		not specified	Uncertain significance (Jul 14, 2023)
X-17800714-C-T		not specified	Uncertain significance (May 15, 2024)
X-17800729-T-A		not specified	Uncertain significance (Oct 27, 2021)
X-17800748-T-C			Benign (Dec 31, 2019)
X-17800768-G-C		not specified	Uncertain significance (Jun 21, 2022)
X-17800783-C-T		not specified	Uncertain significance (Jul 25, 2023)
X-17800793-A-C		not specified	Uncertain significance (Dec 17, 2023)
X-17800809-T-A		not specified	Uncertain significance (Feb 06, 2024)
X-17800825-C-T		not specified	Uncertain significance (Jul 25, 2023)
X-17800827-G-C		not specified	Uncertain significance (Sep 14, 2023)
X-17800833-T-G		not specified	Uncertain significance (Apr 15, 2024)
X-17800835-A-C		not specified	Uncertain significance (Mar 17, 2023)
X-17800846-C-G		not specified	Uncertain significance (May 03, 2023)
X-17800854-A-G		not specified	Uncertain significance (Oct 29, 2021)
X-17800959-C-T		not specified	Uncertain significance (Apr 13, 2022)
X-17800972-C-G		not specified	Likely benign (Sep 16, 2021)
X-17800994-T-G		not specified	Uncertain significance (Mar 18, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAI2	protein_coding	protein_coding	ENST00000545871	1	61289

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.612	0.381	125737	0	3	125740	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0606	217	215	1.01	0.0000165	3492
Missense in Polyphen		29	38.063	0.76189		625
Synonymous	-0.471	102	96.1	1.06	0.00000818	1104
Loss of Function	2.15	1	7.23	0.138	4.57e-7	136

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000112	0.0000980
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000124	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0996

Intolerance Scores

• loftool: 0.243
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.56

Haploinsufficiency Scores

• pHI: 0.783
• hipred: N
• hipred_score: 0.382
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.590

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rai2

Gene ontology

• Biological process: embryo development ending in birth or egg hatching
• Cellular component: cellular_component
• Molecular function: molecular_function;protein binding