RMI2

RecQ mediated genome instability 2

Basic information

Region (hg38): 16:11249619-11381662

Previous symbols: [ "C16orf75" ]

Links

ENSG00000175643 ∙ NCBI:116028 ∙ OMIM:612426 ∙ HGNC:28349 ∙ Uniprot:Q96E14 ∙ 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 RMI2 gene.

• not provided (2 variants)
• Autoimmune hemolytic anemia;Autoimmune thrombocytopenia (2 variants)
• Autoinflammatory syndrome with immunodeficiency (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RMI2 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	2	3	81	8	17	111
Total	2	3	99	8	17

Variants in RMI2

This is a list of pathogenic ClinVar variants found in the RMI2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-11254001-T-C		-	no classification for the single variant (-)
16-11254849-C-G		not specified	Likely benign (Mar 01, 2023)
16-11254862-G-A		not specified	Uncertain significance (Mar 20, 2024)
16-11254875-C-T		Autoinflammatory syndrome with immunodeficiency	Uncertain significance (Dec 02, 2024)
16-11254880-A-G		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
16-11254882-G-A			Benign (Sep 01, 2022)
16-11254902-G-A			Uncertain significance (Feb 10, 2022)
16-11254909-G-C		not specified	Uncertain significance (Apr 28, 2022)
16-11254915-G-A			Benign (Aug 10, 2018)
16-11254919-C-T		Autoinflammatory syndrome with immunodeficiency	Likely pathogenic (Oct 04, 2023)
16-11254961-G-A		not specified	Uncertain significance (Jun 27, 2022)
16-11254968-C-T		not specified	Uncertain significance (Jun 28, 2022)
16-11254991-C-G		not specified	Uncertain significance (Feb 28, 2023)
16-11254997-A-G		not specified	Uncertain significance (Jun 07, 2024)
16-11254998-T-TGCCGC		Autoinflammatory syndrome with immunodeficiency	Pathogenic (Jun 17, 2021)
16-11254998-T-TGCGGC		Autoimmune hemolytic anemia;Autoimmune thrombocytopenia • Autoinflammatory syndrome with immunodeficiency	Pathogenic (Jul 01, 2021)
16-11255013-C-A		not specified	Uncertain significance (Feb 17, 2024)
16-11255016-C-G		not specified	Uncertain significance (Dec 28, 2023)
16-11255016-C-T			Uncertain significance (Jul 19, 2022)
16-11255017-G-T		Malignant lymphoma, large B-cell, diffuse • Neoplasm	Pathogenic (Dec 04, 2023)
16-11255019-A-G		Systemic lupus erythematosus • AUTOINFLAMMATORY SYNDROME, FAMILIAL, WITHOUT IMMUNODEFICIENCY	Pathogenic/Likely pathogenic (Jun 17, 2021)
16-11255025-C-A		Autoinflammatory syndrome with immunodeficiency	Likely pathogenic (Apr 04, 2024)
16-11255040-G-A		not specified	Uncertain significance (Jan 10, 2023)
16-11255046-C-G			Uncertain significance (Jan 01, 2023)
16-11255055-C-G		not specified	Uncertain significance (Feb 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RMI2	protein_coding	protein_coding	ENST00000312499	2	102144

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0190	0.517	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.621	45	34.7	1.30	0.00000157	909
Missense in Polyphen		14	13.838	1.0117		290
Synonymous	-1.49	19	12.3	1.54	5.85e-7	316
Loss of Function	-0.350	2	1.53	1.31	6.47e-8	41

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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. It is required to regulate sister chromatid segregation and to limit DNA crossover. Essential for the stability, localization, and function of BLM, TOP3A, and complexes containing BLM. In the RMI complex, it is required to target BLM to chromatin and stress-induced nuclear foci and mitotic phosphorylation of BLM. {ECO:0000269|PubMed:18923082, ECO:0000269|PubMed:18923083, ECO:0000269|PubMed:27977684}.
• Disease: DISEASE: Note=A homozygous deletion of RMI2 has been found in a family with a Bloom-like syndrome and is probable responsible for the phenotype. Patients manifest depigmented skin lesions, multiple cafe-au-lait macules, and growth deficiency. Cells from affected individuals show a high rate of sister chromatid exchange and increased chromosomal breaks. {ECO:0000269|PubMed:27977684}.
• 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;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: 0.114

Haploinsufficiency Scores

• pHI: 0.402
• hipred: Y
• hipred_score: 0.807
• ghis: 0.687

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rmi2

Gene ontology

• Biological process: DNA replication;DNA repair;regulation of sister chromatid segregation;negative regulation of double-strand break repair via homologous recombination
• Cellular component: nucleoplasm;cytosol;nuclear speck
• Molecular function: DNA binding;protein binding