RAD9A

RAD9 checkpoint clamp component A, the group of Checkpoint clamp complex

Basic information

Region (hg38): 11:67317871-67398410

Previous symbols: [ "RAD9" ]

Links

ENSG00000172613 ∙ NCBI:5883 ∙ OMIM:603761 ∙ HGNC:9827 ∙ Uniprot:Q99638 ∙ 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 RAD9A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAD9A 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						0
missense			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	0

Variants in RAD9A

This is a list of pathogenic ClinVar variants found in the RAD9A region.

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

Position	Type	Phenotype	Significance	ClinVar
11-67352011-T-C		not specified	Uncertain significance (Mar 15, 2024)
11-67352749-G-T		not specified	Uncertain significance (Dec 13, 2022)
11-67352793-C-A		not specified	Uncertain significance (Sep 26, 2023)
11-67353001-G-A			Likely benign (Jan 01, 2023)
11-67353009-A-G		not specified	Uncertain significance (Aug 30, 2021)
11-67353345-C-T		not specified	Uncertain significance (Sep 06, 2022)
11-67353365-G-A		not specified	Uncertain significance (Oct 26, 2022)
11-67353371-G-C		not specified	Uncertain significance (Mar 31, 2024)
11-67365138-A-G		Cold-induced sweating syndrome 2	Pathogenic (Jun 15, 2010)
11-67365147-GAGCCCCC-G		not specified	Benign (May 20, 2022)
11-67365215-T-C		not specified	Uncertain significance (Jun 07, 2024)
11-67365221-G-A		not specified	Uncertain significance (Oct 05, 2021)
11-67365224-C-A		Cold-induced sweating syndrome 2	Pathogenic (Jun 27, 2006)
11-67365265-G-A		CLCF1-related disorder	Likely benign (May 25, 2019)
11-67365327-G-A		not specified	Uncertain significance (Mar 28, 2024)
11-67365366-C-T		not specified	Uncertain significance (Apr 07, 2022)
11-67365422-C-T		not specified	Uncertain significance (Jun 29, 2022)
11-67365425-C-T		not specified	Uncertain significance (Sep 16, 2021)
11-67365426-G-A		not specified	Uncertain significance (Jan 23, 2024)
11-67365427-C-T			Likely benign (Aug 16, 2018)
11-67365450-G-C		not specified	Uncertain significance (Mar 20, 2024)
11-67365456-G-A		not specified	Uncertain significance (Dec 11, 2023)
11-67365493-G-T		Cold-induced sweating syndrome 2	Pathogenic (Jun 27, 2006)
11-67365521-T-C		not specified	Uncertain significance (May 30, 2024)
11-67365523-G-A			Likely benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAD9A	protein_coding	protein_coding	ENST00000307980	11	6706

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000403	0.839	125717	0	30	125747	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00665	246	246	1.00	0.0000153	2512
Missense in Polyphen		77	91.028	0.84589		990
Synonymous	-1.96	127	102	1.25	0.00000622	809
Loss of Function	1.41	11	17.3	0.635	7.35e-7	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000482	0.000428
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000112	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000112	0.000109
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the 9-1-1 cell-cycle checkpoint response complex that plays a major role in DNA repair. The 9-1-1 complex is recruited to DNA lesion upon damage by the RAD17-replication factor C (RFC) clamp loader complex. Acts then as a sliding clamp platform on DNA for several proteins involved in long-patch base excision repair (LP-BER). The 9-1-1 complex stimulates DNA polymerase beta (POLB) activity by increasing its affinity for the 3'-OH end of the primer-template and stabilizes POLB to those sites where LP-BER proceeds; endonuclease FEN1 cleavage activity on substrates with double, nick, or gap flaps of distinct sequences and lengths; and DNA ligase I (LIG1) on long-patch base excision repair substrates. The 9-1-1 complex is necessary for the recruitment of RHNO1 to sites of double-stranded breaks (DSB) occurring during the S phase. RAD9A possesses 3'->5' double stranded DNA exonuclease activity. Its phosphorylation by PRKCD may be required for the formation of the 9-1-1 complex. {ECO:0000269|PubMed:10713044, ECO:0000269|PubMed:21659603}.
• Pathway: Cellular senescence - Homo sapiens (human);Androgen receptor signaling pathway;miRNA Regulation of DNA Damage Response;ATM Signaling Pathway;ATR Signaling;DNA IR-Double Strand Breaks (DSBs) and cellular response via ATM;DNA Damage Response;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;role of brca1 brca2 and atr in cancer susceptibility;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;Fanconi anemia pathway;Regulation of TP53 Activity through Phosphorylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Cell Cycle;Regulation of Telomerase;Processing of DNA double-strand break ends;ATM pathway;ATR signaling pathway;Presynaptic phase of homologous DNA pairing and strand exchange;Homologous DNA Pairing and Strand Exchange;HDR through Homologous Recombination (HRR) (Consensus)

Recessive Scores

• pRec: 0.197

Intolerance Scores

• loftool: 0.588
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.7

Haploinsufficiency Scores

• pHI: 0.511
• hipred: Y
• hipred_score: 0.740
• ghis: 0.534

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.972

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rad9a
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); pigmentation phenotype; neoplasm; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system 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)

Gene ontology

• Biological process: DNA replication checkpoint;DNA damage checkpoint;DNA repair;cellular response to DNA damage stimulus;intra-S DNA damage checkpoint;cellular response to ionizing radiation;nucleic acid phosphodiester bond hydrolysis;positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage
• Cellular component: nucleus;nucleoplasm;cytoplasm;checkpoint clamp complex
• Molecular function: protein binding;3'-5' exonuclease activity;exodeoxyribonuclease III activity;SH3 domain binding;enzyme binding;protein kinase binding;histone deacetylase binding