RBM7

RNA binding motif protein 7, the group of RNA binding motif containing|Nuclear exosome targeting complex

Basic information

Region (hg38): 11:114400030-114414203

Links

ENSG00000076053 ∙ NCBI:10179 ∙ OMIM:612413 ∙ HGNC:9904 ∙ Uniprot:Q9Y580 ∙ 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 RBM7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBM7 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	21	0	0

Variants in RBM7

This is a list of pathogenic ClinVar variants found in the RBM7 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-114400052-T-C		not specified	Uncertain significance (Aug 17, 2021)
11-114400681-G-C			Uncertain significance (Oct 01, 2023)
11-114400687-G-A		not specified	Uncertain significance (Feb 14, 2024)
11-114400703-C-T		not specified	Uncertain significance (Sep 28, 2022)
11-114401711-T-C		not specified	Uncertain significance (Nov 09, 2023)
11-114401741-G-A		not specified	Uncertain significance (Dec 01, 2022)
11-114401834-G-A		not specified	Uncertain significance (Jun 22, 2021)
11-114402893-C-T		not specified	Uncertain significance (Aug 07, 2024)
11-114405727-T-G		not specified	Uncertain significance (Jan 16, 2024)
11-114405768-C-T		not specified	Uncertain significance (Dec 26, 2023)
11-114405787-G-C		not specified	Uncertain significance (Sep 30, 2024)
11-114407445-A-T		not specified	Uncertain significance (Feb 22, 2025)
11-114407466-A-C		not specified	Uncertain significance (Sep 13, 2023)
11-114407551-A-G		not specified	Uncertain significance (Dec 09, 2023)
11-114407569-A-G		not specified	Uncertain significance (Feb 20, 2025)
11-114407595-C-G		not specified	Uncertain significance (Oct 22, 2021)
11-114407609-A-C		not specified	Uncertain significance (Dec 03, 2024)
11-114407649-C-T		not specified	Uncertain significance (Aug 21, 2024)
11-114407650-G-A		not specified	Uncertain significance (Feb 26, 2025)
11-114407683-A-G			Uncertain significance (Dec 01, 2019)
11-114407695-G-A		not specified	Uncertain significance (May 18, 2023)
11-114407721-G-A		not specified	Uncertain significance (Oct 06, 2022)
11-114407790-C-T		not specified	Uncertain significance (Apr 09, 2024)
11-114407791-G-T		not specified	Uncertain significance (Jun 16, 2024)
11-114407800-G-A		not specified	Uncertain significance (Dec 18, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBM7	protein_coding	protein_coding	ENST00000540163	5	14174

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.648	0.351	125740	0	5	125745	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.825	118	146	0.808	0.00000727	1752
Missense in Polyphen		17	34.903	0.48706		466
Synonymous	-0.380	53	49.6	1.07	0.00000235	481
Loss of Function	2.68	2	12.0	0.167	5.06e-7	154

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)	0.0000445	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Subunit of the trimeric nuclear exosome targeting (NEXT) complex, a complex that directs a subset of non-coding short-lived RNAs for exosomal degradation. The RNA exosome is fundamental for the degradation of RNA in eukaryotic nuclei. Substrate targeting is facilitated by its cofactor MTREX, which links to RNA-binding protein adapters (PubMed:27871484). Possible involved in germ cell RNA processing and meiosis (Probable). {ECO:0000269|PubMed:27871484, ECO:0000305|PubMed:12634307}.

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.386
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.249
• hipred: N
• hipred_score: 0.458
• ghis: 0.490

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.970

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rbm7

Zebrafish Information Network

• Gene name: rbm7
• Affected structure: motor neuron
• Phenotype tag: abnormal
• Phenotype quality: branchiness

Gene ontology

• Biological process: regulation of alternative mRNA splicing, via spliceosome;meiotic cell cycle
• Cellular component: nucleus;nucleoplasm;nucleolus
• Molecular function: RNA binding;single-stranded RNA binding;protein binding