RMRP

RNA component of mitochondrial RNA processing endoribonuclease

Basic information

Region (hg38): 9:35657754-35658017

Previous symbols: [ "CHH" ]

Links

ENSG00000277027 ∙ NCBI:6023 ∙ OMIM:157660 ∙ HGNC:10031 ∙ ∙ ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Anauxetic dysplasia 1; Cartilage-hair hypoplasia; Metaphyseal dysplasia without hypotrichosis	AR	Allergy/Immunology/Infectious; Hematologic; Oncologic	There 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 described	Allergy/Immunology/Infectious; Dermatologic; Hematologic; Musculoskeletal; Neurologic; Oncologic	14284412; 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	2	5			8
splice region						0
non coding	22	21	316	8	3	370
Total	23	23	321	8	3

Highest pathogenic variant AF is 0.000151

Variants in RMRP

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

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

Position	Type	Phenotype	Significance	ClinVar
9-35657755-C-T		Anauxetic dysplasia • Metaphyseal chondrodysplasia, McKusick type	Uncertain significance (Aug 02, 2022)
9-35657756-C-A		Metaphyseal chondrodysplasia, McKusick type • Anauxetic dysplasia • Metaphyseal chondrodysplasia, McKusick type;Anauxetic dysplasia 1;Metaphyseal dysplasia without hypotrichosis	Pathogenic (Jan 20, 2024)
9-35657756-C-G		Anauxetic dysplasia	Pathogenic/Likely pathogenic (Aug 23, 2022)
9-35657756-C-T		Anauxetic dysplasia	Uncertain significance (Aug 01, 2022)
9-35657756-CG-TT		Anauxetic dysplasia	Uncertain significance (Jul 05, 2022)
9-35657757-G-A		Anauxetic dysplasia	Uncertain significance (Apr 16, 2022)
9-35657757-G-C		Metaphyseal chondrodysplasia, McKusick type • Anauxetic dysplasia	Uncertain significance (Jul 16, 2022)
9-35657758-C-T		Anauxetic dysplasia • Metaphyseal chondrodysplasia, McKusick type • not specified	Uncertain significance (Aug 02, 2022)
9-35657759-G-C		Anauxetic dysplasia	Uncertain significance (Dec 02, 2023)
9-35657760-C-T		Anauxetic dysplasia	Uncertain significance (Aug 30, 2021)
9-35657761-T-C		Anauxetic dysplasia	Uncertain significance (Apr 18, 2022)
9-35657764-G-C		Anauxetic dysplasia 1 • Metaphyseal chondrodysplasia, McKusick type	Uncertain significance (Jun 07, 2017)
9-35657764-G-T		Metaphyseal chondrodysplasia, McKusick type	Uncertain significance (Jun 19, 2017)
9-35657765-A-C		Anauxetic dysplasia	Uncertain significance (Oct 25, 2022)
9-35657765-AATGAGCCCC-A		Anauxetic dysplasia	Uncertain significance (May 20, 2021)
9-35657766-A-C		not specified	Uncertain significance (Jul 28, 2023)
9-35657766-A-G		Anauxetic dysplasia	Uncertain significance (Feb 28, 2022)
9-35657768-G-A		Anauxetic dysplasia	Uncertain significance (Jul 19, 2022)
9-35657770-G-A		Metaphyseal chondrodysplasia, McKusick type	Uncertain significance (Jul 20, 2017)
9-35657773-C-T		Anauxetic dysplasia • Metaphyseal chondrodysplasia, McKusick type	Uncertain significance (Aug 31, 2021)
9-35657774-C-G		Metaphyseal chondrodysplasia, McKusick type	Pathogenic (Jan 25, 2024)
9-35657775-G-A		Metaphyseal chondrodysplasia, McKusick type	Uncertain significance (Apr 02, 2018)
9-35657775-G-C		Anauxetic dysplasia	Uncertain significance (Apr 27, 2021)
9-35657775-GTGTGGT-G		Metaphyseal chondrodysplasia, McKusick type	Uncertain significance (Sep 08, 2017)
9-35657776-T-C		Metaphyseal chondrodysplasia, McKusick type • Anauxetic dysplasia • Anauxetic dysplasia 1;Metaphyseal chondrodysplasia, McKusick type;Metaphyseal dysplasia without hypotrichosis • RMRP-related disorder	Pathogenic/Likely pathogenic (Jan 16, 2024)

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

• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.506

Essentials

• 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)