RMI1

RecQ mediated genome instability 1

Basic information

Region (hg38): 9:83980798-84004074

Previous symbols: [ "C9orf76" ]

Links

ENSG00000178966 ∙ NCBI:80010 ∙ OMIM:610404 ∙ HGNC:25764 ∙ Uniprot:Q9H9A7 ∙ 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 RMI1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RMI1 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					2	2
missense			22	7	4	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	7	6

Variants in RMI1

This is a list of pathogenic ClinVar variants found in the RMI1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-84001041-C-T			Likely benign (Feb 01, 2023)
9-84001044-G-A		not specified	Uncertain significance (Mar 28, 2024)
9-84001057-C-T		not specified	Likely benign (Sep 09, 2021)
9-84001105-A-C		not specified	Uncertain significance (Jan 17, 2024)
9-84001134-A-G		not specified	Uncertain significance (Feb 21, 2024)
9-84001224-G-A		not specified	Uncertain significance (Aug 17, 2022)
9-84001258-C-T		not specified	Uncertain significance (Mar 07, 2024)
9-84001260-T-G		not specified	Uncertain significance (Jan 24, 2024)
9-84001416-G-A		not specified	Uncertain significance (Apr 04, 2024)
9-84001437-T-A		not specified	Uncertain significance (May 26, 2024)
9-84001441-A-G		not specified	Uncertain significance (Mar 16, 2022)
9-84001452-A-G		not specified	Uncertain significance (Sep 12, 2023)
9-84001463-T-G		not specified	Uncertain significance (Jun 03, 2022)
9-84001504-T-C		not specified	Uncertain significance (Mar 25, 2024)
9-84001507-C-G		not specified	Uncertain significance (Apr 23, 2024)
9-84001512-C-T		not specified	Uncertain significance (Jun 30, 2023)
9-84001528-T-C		RMI1-related disorder	Likely benign (Feb 22, 2022)
9-84001536-C-A		not specified	Uncertain significance (Aug 02, 2022)
9-84001578-T-C		RMI1-related disorder	Benign (Jan 06, 2020)
9-84001596-G-C		not specified	Uncertain significance (Dec 01, 2022)
9-84001609-C-T		not specified	Uncertain significance (Apr 08, 2022)
9-84001687-A-G		not specified	Uncertain significance (Aug 15, 2023)
9-84001693-T-C		not specified	Uncertain significance (Dec 13, 2023)
9-84001824-A-G		not specified	Uncertain significance (Jun 22, 2024)
9-84001836-A-G		RMI1-related disorder	Benign (Jun 30, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RMI1	protein_coding	protein_coding	ENST00000325875	1	23360

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000366	0.949	125662	0	69	125731	0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.349	293	310	0.944	0.0000144	4126
Missense in Polyphen		41	66.216	0.61918		874
Synonymous	0.0450	113	114	0.995	0.00000552	1186
Loss of Function	1.84	12	21.1	0.568	0.00000115	277

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000457	0.000456
Ashkenazi Jewish	0.00	0.00
East Asian	0.000276	0.000272
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000345	0.000343
Middle Eastern	0.000276	0.000272
South Asian	0.000396	0.000392
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential component of the RMI complex, a complex that plays an important role in the processing of homologous recombination intermediates to limit DNA crossover formation in cells. Promotes TOP3A binding to double Holliday junctions (DHJ) and hence stimulates TOP3A-mediated dissolution. Required for BLM phosphorylation during mitosis. Within the BLM complex, required for BLM and TOP3A stability. {ECO:0000269|PubMed:15775963, ECO:0000269|PubMed:16537486, ECO:0000269|PubMed:16595695}.
• Pathway: Fanconi anemia pathway - Homo sapiens (human);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;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;Presynaptic phase of homologous DNA pairing and strand exchange;Homologous DNA Pairing and Strand Exchange;Resolution of D-loop Structures through Holliday Junction Intermediates;Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA);Resolution of D-Loop Structures;HDR through Homologous Recombination (HRR) (Consensus)

Recessive Scores

• pRec: 0.0967

Intolerance Scores

• loftool: 0.787
• rvis_EVS: 0.67
• rvis_percentile_EVS: 84.61

Haploinsufficiency Scores

• pHI: 0.714
• hipred: Y
• hipred_score: 0.537
• ghis: 0.540

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.960

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rmi1
• Phenotype: homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue 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); growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype

Gene ontology

• Biological process: resolution of meiotic recombination intermediates;double-strand break repair via homologous recombination;reduction of food intake in response to dietary excess;DNA replication;response to glucose;multicellular organism growth;glucose homeostasis
• Cellular component: nucleoplasm;nuclear body;RecQ helicase-Topo III complex
• Molecular function: nucleotide binding;protein binding