RAD9B

protein-coding

RAD9 checkpoint clamp component B

Gene summary

Predicted to be involved in DNA integrity checkpoint signaling; DNA repair; and cellular response to ionizing radiation. Located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001286535.2

Inheritance

—

ClinVar variants

P:7U:48B:6

Top phenotype

Neural tube defect

gnomAD constraint

pLI —, LoF o/e 0.94

Max pathogenic AF

—

Genomic locus

chr12:110,501,655-110,533,556

External References & Databases

Ensembl (ENSG00000151164)

Transcript & Mutation Effects

hg38 • Region Span ~31.9 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RAD9B variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 47

Neural tube defectTotal: 7

RAD9B-related disorderTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001286535.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense		5 clinvar	47 clinvar	5 clinvar		57
nonsense						0
start loss						0
frameshift	2 clinvar					2
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	2	5	48	6	0	61

Highest pathogenic variant AF is 0.00007931472

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001286535.2	RefSeq	NP_001273464.1	11	MANE Select
ENST00000409300.6	Ensembl	ENSP00000386434.1	11	MANE Select
NM_001286531.2	RefSeq	NP_001273460.1	9	Standard
NM_001286532.2	RefSeq	NP_001273461.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

DNA repair
intra-S DNA damage checkpoint
cellular response to ionizing radiation
nucleic acid phosphodiester bond hydrolysis

Molecular Function

protein binding
3'-5' exonuclease activity

Cellular Component

nucleoplasm
checkpoint clamp complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000392672
Coding exons: 12
Length: 30432
Individuals with no LoFs: 125563
Homozygous LoFs: 0
Heterozygous LoFs: 34
Defined: 125597
p: 0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.321	187	200	0.936	0.00000877	2814
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00038	0.00037	rare
Latino/Admixed American	0.00021	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000057	0.000054	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.00015	0.00013	rare
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0952

Intolerance Scores

LoFtool: 0.854
RVIS EVS: 0.64
RVIS percentile EVS: 83.9

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.355

Gene Damage Prediction

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