RAD9B

RAD9 checkpoint clamp component B

Basic information

Region (hg38): 12:110501655-110533556

Links

ENSG00000151164 ∙ NCBI:144715 ∙ OMIM:608368 ∙ HGNC:21700 ∙ Uniprot:Q6WBX8 ∙ 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 RAD9B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAD9B 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				1		1
missense			13	3		16
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2	1		3
Total	0	0	15	5	1

Variants in RAD9B

This is a list of pathogenic ClinVar variants found in the RAD9B region.

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

Position	Type	Phenotype	Significance	ClinVar
12-110502347-A-G		not specified	Uncertain significance (Dec 19, 2022)
12-110502363-T-C		not specified	Uncertain significance (Oct 03, 2023)
12-110502365-A-G		Neural tube defect	Likely pathogenic (-)
12-110503836-G-A		not specified	Uncertain significance (Sep 14, 2022)
12-110503850-T-C		not specified	Likely benign (Dec 12, 2022)
12-110505623-C-G		not specified	Uncertain significance (Feb 07, 2023)
12-110505672-C-G		not specified	Uncertain significance (May 31, 2023)
12-110505675-C-T		RAD9B-related disorder	Likely benign (Apr 06, 2022)
12-110505719-A-C		not specified	Uncertain significance (Mar 02, 2023)
12-110505723-A-C		not specified	Uncertain significance (Jul 19, 2023)
12-110506636-A-C		RAD9B-related disorder	Likely benign (Mar 21, 2022)
12-110506640-T-C		not specified	Uncertain significance (May 16, 2023)
12-110506641-A-G		Neural tube defect	Likely pathogenic (-)
12-110512779-G-T		not specified	Uncertain significance (May 16, 2023)
12-110515087-C-G		RAD9B-related disorder	Likely benign (Mar 23, 2023)
12-110515135-A-G		not specified	Uncertain significance (Jun 22, 2023)
12-110518676-A-C		not specified	Uncertain significance (Feb 28, 2023)
12-110518685-A-G		not specified	Likely benign (Feb 28, 2024)
12-110518703-T-C		not specified	Uncertain significance (Apr 25, 2023)
12-110518725-T-A		Neural tube defect	Likely pathogenic (-)
12-110518741-G-A		Neural tube defect	Likely pathogenic (-)
12-110518745-T-G		not specified	Uncertain significance (Oct 12, 2021)
12-110519873-G-A		not specified	Uncertain significance (Mar 28, 2024)
12-110522239-CA-C		Neural tube defect	Pathogenic (-)
12-110522263-T-C		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAD9B	protein_coding	protein_coding	ENST00000392672	12	30432

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.02e-13	0.0403	125563	0	34	125597	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.321	187	200	0.936	0.00000877	2814
Missense in Polyphen		45	55.2	0.81521		856
Synonymous	0.548	61	66.7	0.915	0.00000310	749
Loss of Function	0.250	20	21.2	0.941	0.00000107	292

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000592	0.000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000567	0.0000544
Finnish	0.0000470	0.0000462
European (Non-Finnish)	0.000119	0.000115
Middle Eastern	0.0000567	0.0000544
South Asian	0.000151	0.000131
Other	0.000342	0.000326

dbNSFP

Source: dbNSFP

• Pathway: Cellular senescence - Homo sapiens (human);ATR Signaling;HDR through Single Strand Annealing (SSA);HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA);DNA Repair;Gene expression (Transcription);DNA Double-Strand Break Repair;Generic Transcription Pathway;Homology Directed Repair;RNA Polymerase II Transcription;G2/M DNA damage checkpoint;Activation of ATR in response to replication stress;G2/M Checkpoints;Cell Cycle Checkpoints;Regulation of TP53 Activity through Phosphorylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Cell Cycle;Processing of DNA double-strand break ends;Presynaptic phase of homologous DNA pairing and strand exchange;Homologous DNA Pairing and Strand Exchange;HDR through Homologous Recombination (HRR) (Consensus)

Recessive Scores

• pRec: 0.0952

Intolerance Scores

• loftool: 0.854
• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.9

Haploinsufficiency Scores

• pHI: 0.271
• hipred: N
• hipred_score: 0.333

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.355

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rad9b
• Phenotype: growth/size/body region phenotype; cellular 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); 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); embryo phenotype

Gene ontology

• Biological process: DNA repair;intra-S DNA damage checkpoint;cellular response to ionizing radiation;nucleic acid phosphodiester bond hydrolysis
• Cellular component: nucleoplasm;checkpoint clamp complex
• Molecular function: protein binding;3'-5' exonuclease activity