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RMRP

RNA component of mitochondrial RNA processing endoribonuclease

Basic information

Previous symbols: [ "CHH" ]

Links

ENSG00000277027NCBI:6023OMIM:157660HGNC:10031GenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • cartilage-hair hypoplasia (Definitive), mode of inheritance: AR
  • cartilage-hair hypoplasia (Definitive), mode of inheritance: AR
  • cartilage-hair hypoplasia (Definitive), mode of inheritance: AR
  • cartilage-hair hypoplasia (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Anauxetic dysplasia 1; Cartilage-hair hypoplasia; Metaphyseal dysplasia without hypotrichosisARAllergy/Immunology/Infectious; Hematologic; OncologicThere is a wide range of manifestations and severity, and while the disorder may be frequently (though not always) easily clinically recognizable, there is an increased risk reported of hematologic, immunologic, and oncologic complications, and surveillance and prompt treatment may be beneficial; HSCT has been describedAllergy/Immunology/Infectious; Dermatologic; Hematologic; Musculoskeletal; Neurologic; Oncologic14284412; 3521972; 1743218; 1789294; 1442902; 1290847; 1404295; 8444246; 9809821; 10494084; 10064668; 11207361; 11940090; 16252239; 16097009; 16832578; 18280854; 18698627; 18280853; 19150606; 20375313; 20538026; 21063072; 22420014; 22987807; 30561899

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RMRP gene.

  • Anauxetic dysplasia (336 variants)
  • Metaphyseal chondrodysplasia, McKusick type (157 variants)
  • not specified (22 variants)
  • not provided (21 variants)
  • Anauxetic dysplasia 1;Metaphyseal dysplasia without hypotrichosis;Metaphyseal chondrodysplasia, McKusick type (9 variants)
  • Anauxetic dysplasia 1;Metaphyseal chondrodysplasia, McKusick type;Metaphyseal dysplasia without hypotrichosis (7 variants)
  • RMRP-related condition (6 variants)
  • Metaphyseal dysplasia without hypotrichosis (5 variants)
  • Anauxetic dysplasia 1 (5 variants)
  • Metaphyseal chondrodysplasia, McKusick type;Anauxetic dysplasia 1;Metaphyseal dysplasia without hypotrichosis (5 variants)
  • Metaphyseal chondrodysplasia, McKusick type;Metaphyseal dysplasia without hypotrichosis;Anauxetic dysplasia 1 (4 variants)
  • Cartilage-Hair Hypoplasia-Anauxetic Dysplasia Spectrum Disorders (2 variants)
  • Metaphyseal dysplasia without hypotrichosis;Anauxetic dysplasia 1;Metaphyseal chondrodysplasia, McKusick type (1 variants)
  • Metaphyseal dysplasia without hypotrichosis;Metaphyseal chondrodysplasia, McKusick type;Anauxetic dysplasia 1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RMRP 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
0
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
1
clinvar
2
clinvar
5
clinvar
8
splice region
0
non coding
22
clinvar
21
clinvar
316
clinvar
8
clinvar
3
clinvar
370
Total 23 23 321 8 3

Highest pathogenic variant AF is 0.000151

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Function
FUNCTION: Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. Possesses nucleoside-diphosphate kinase, serine/threonine-specific protein kinase, geranyl and farnesyl pyrophosphate kinase, histidine protein kinase and 3'-5' exonuclease activities. Involved in cell proliferation, differentiation and development, signal transduction, G protein- coupled receptor endocytosis, and gene expression. Required for neural development including neural patterning and cell fate determination. During GZMA-mediated cell death, works in concert with TREX1. NME1 nicks one strand of DNA and TREX1 removes bases from the free 3' end to enhance DNA damage and prevent DNA end reannealing and rapid repair. {ECO:0000269|PubMed:12628186, ECO:0000269|PubMed:16818237, ECO:0000269|PubMed:8810265}.;
Pathway
Ribosome biogenesis in eukaryotes - Homo sapiens (human) (Consensus)

Recessive Scores

pRec
0.461

Intolerance Scores

loftool
rvis_EVS
-0.12
rvis_percentile_EVS
44.54

Haploinsufficiency Scores

pHI
hipred
Y
hipred_score
0.506
ghis

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
gene_indispensability_pred
E
gene_indispensability_score
0.914

Mouse Genome Informatics

Gene name
Rmrp
Phenotype
normal phenotype; 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);