RAD17

RAD17 checkpoint clamp loader component

Basic information

Region (hg38): 5:69369292-69414801

Links

ENSG00000152942 ∙ NCBI:5884 ∙ OMIM:603139 ∙ HGNC:9807 ∙ Uniprot:O75943 ∙ 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 RAD17 gene.

• Inborn genetic diseases (22 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAD17 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			21	1		22
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 RAD17

This is a list of pathogenic ClinVar variants found in the RAD17 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-69371535-G-T		not specified	Uncertain significance (Feb 21, 2024)
5-69371550-C-T		not specified	Uncertain significance (Jan 08, 2024)
5-69373969-T-C		not specified	Uncertain significance (Jul 12, 2023)
5-69374031-A-G		not specified	Uncertain significance (Feb 14, 2023)
5-69374676-T-A		not specified	Uncertain significance (Mar 24, 2023)
5-69374682-G-C		not specified	Uncertain significance (Aug 13, 2021)
5-69381919-A-G		not specified	Uncertain significance (Dec 03, 2021)
5-69382055-C-G		not specified	Uncertain significance (Jun 05, 2023)
5-69386212-T-C		not specified	Uncertain significance (Aug 08, 2023)
5-69386224-C-T		not specified	Uncertain significance (Apr 18, 2023)
5-69386401-A-G		not specified	Uncertain significance (Dec 06, 2022)
5-69386404-C-T		not specified	Uncertain significance (Jan 26, 2022)
5-69386440-G-A		not specified	Uncertain significance (Mar 24, 2023)
5-69389070-C-G		not specified	Uncertain significance (Nov 02, 2023)
5-69391884-G-A		not specified	Uncertain significance (Jan 26, 2023)
5-69393367-T-A		not specified	Uncertain significance (Jan 18, 2023)
5-69393375-A-G		not specified	Uncertain significance (Jul 20, 2021)
5-69393495-T-C		not specified	Uncertain significance (Mar 20, 2023)
5-69396400-C-T		not specified	Likely benign (Feb 22, 2023)
5-69396404-C-G		not specified	Uncertain significance (Jan 23, 2024)
5-69396500-G-A		not specified	Uncertain significance (Jan 04, 2024)
5-69400053-G-A		not specified	Uncertain significance (May 15, 2023)
5-69400069-A-G		not specified	Likely benign (Mar 29, 2016)
5-69400112-C-T		not specified	Uncertain significance (Apr 26, 2023)
5-69400127-T-A		not specified	Uncertain significance (Sep 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAD17	protein_coding	protein_coding	ENST00000509734	16	45509

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0569	0.943	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.618	310	342	0.906	0.0000167	4443
Missense in Polyphen		60	86.614	0.69273		1193
Synonymous	-0.00516	120	120	1.00	0.00000595	1268
Loss of Function	4.22	10	38.1	0.262	0.00000207	490

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000190	0.000189
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential for sustained cell growth, maintenance of chromosomal stability, and ATR-dependent checkpoint activation upon DNA damage. Has a weak ATPase activity required for binding to chromatin. Participates in the recruitment of the RAD1-RAD9- HUS1 complex and RHNO1 onto chromatin, and in CHEK1 activation. May also serve as a sensor of DNA replication progression, and may be involved in homologous recombination. {ECO:0000269|PubMed:10208430, ECO:0000269|PubMed:11418864, ECO:0000269|PubMed:11687627, ECO:0000269|PubMed:11799063, ECO:0000269|PubMed:12578958, ECO:0000269|PubMed:12672690, ECO:0000269|PubMed:14500819, ECO:0000269|PubMed:14624239, ECO:0000269|PubMed:15235112, ECO:0000269|PubMed:15538388, ECO:0000269|PubMed:21659603}.
• Pathway: miRNA Regulation of DNA Damage Response;Gastric Cancer Network 2;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;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: 0.207

Intolerance Scores

• loftool: 0.936
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.78

Haploinsufficiency Scores

• pHI: 0.377
• hipred: Y
• hipred_score: 0.648
• ghis: 0.544

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.581

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rad17
• Phenotype: embryo phenotype; liver/biliary system phenotype; 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); 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); craniofacial phenotype

Gene ontology

• Biological process: DNA replication checkpoint;DNA damage checkpoint;DNA replication;DNA repair;cellular response to DNA damage stimulus;mitotic cell cycle checkpoint;negative regulation of DNA replication;mitotic DNA replication checkpoint;regulation of phosphorylation
• Cellular component: chromosome, telomeric region;nuclear chromatin;nucleus;nucleoplasm;nucleolus;Rad17 RFC-like complex
• Molecular function: chromatin binding;DNA clamp loader activity;protein binding;ATP binding