RMI1

protein-coding

RecQ mediated genome instability 1

Gene summary

Predicted to enable nucleotide binding activity. Involved in double-strand break repair via homologous recombination and resolution of DNA recombination intermediates. Located in nuclear body. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C9orf76

MANE transcript

NM_001358291.2

Inheritance

—

ClinVar variants

P:1U:63B:22

Top phenotype

RMI1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.57

Max pathogenic AF

—

Genomic locus

chr9:83,980,798-84,004,074

External References & Databases

Ensembl (ENSG00000178966)

Transcript & Mutation Effects

hg38 • Region Span ~23.3 kb

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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 RMI1 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 72

RMI1-related disorderTotal: 7

not providedTotal: 6

Olaparib responseTotal: 1

Colorectal cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001358291.2. 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				2 clinvar	2 clinvar	4
missense			62 clinvar	15 clinvar	3 clinvar	80
nonsense						0
start loss						0
frameshift		1 clinvar	1 clinvar			2
splice donor/acceptor (+/-2bp)						0
Total	0	1	63	17	5	86

Highest pathogenic variant AF is 0.00000871053

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001358291.2	RefSeq	NP_001345220.1	1	MANE Select
ENST00000445877.6	Ensembl	ENSP00000402433.2	1	MANE Select
NM_001358292.2	RefSeq	NP_001345221.1	1	Standard
NM_001358293.2	RefSeq	NP_001345222.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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)

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

Molecular Function

nucleotide binding
protein binding

Cellular Component

nucleoplasm
nuclear body
RecQ helicase-Topo III complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000325875
Coding exons: 1
Length: 23360
Individuals with no LoFs: 125662
Homozygous LoFs: 0
Heterozygous LoFs: 69
Defined: 125731
p: 0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.349	293	310	0.944	0.0000144	4126
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00028	0.00027	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00035	0.00034	rare
South Asian	0.00040	0.00039	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0967

Intolerance Scores

LoFtool: 0.787
RVIS EVS: 0.67
RVIS percentile EVS: 84.61

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.960

Gene Damage Prediction

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