RBM17

RNA binding motif protein 17, the group of RNA binding motif containing|G-patch domain containing|Spliceosomal A complex

Basic information

Region (hg38): 10:6089033-6117457

Links

ENSG00000134453 ∙ NCBI:84991 ∙ OMIM:606935 ∙ HGNC:16944 ∙ Uniprot:Q96I25 ∙ 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 RBM17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBM17 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					1	1
missense			7			7
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	1

Variants in RBM17

This is a list of pathogenic ClinVar variants found in the RBM17 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-6101335-C-T		not specified	Uncertain significance (Feb 22, 2024)
10-6101383-T-G		not specified	Uncertain significance (Jul 09, 2021)
10-6104997-A-G		not specified	Uncertain significance (Sep 16, 2021)
10-6105011-T-A		not specified	Uncertain significance (May 20, 2024)
10-6105015-G-A		not specified	Uncertain significance (Nov 13, 2023)
10-6108688-A-G		not specified	Uncertain significance (Mar 21, 2023)
10-6108737-A-G		not specified	Uncertain significance (Feb 05, 2024)
10-6112345-C-T			Benign (Jan 25, 2018)
10-6114091-G-T			Uncertain significance (Apr 14, 2023)
10-6114122-A-G		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBM17	protein_coding	protein_coding	ENST00000446108	11	28471

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000188	125493	0	1	125494	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.10	98	231	0.425	0.0000131	2605
Missense in Polyphen		26	85.481	0.30416		973
Synonymous	-0.190	88	85.8	1.03	0.00000501	780
Loss of Function	4.59	0	24.5	0.00	0.00000142	284

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)	0.00000880	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Splice factor that binds to the single-stranded 3'AG at the exon/intron border and promotes its utilization in the second catalytic step. Involved in the regulation of alternative splicing and the utilization of cryptic splice sites. Promotes the utilization of a cryptic splice site created by the beta-110 mutation in the HBB gene. The resulting frameshift leads to sickle cell anemia. {ECO:0000269|PubMed:12015979, ECO:0000269|PubMed:17589525}.
• Pathway: Spliceosome - Homo sapiens (human);mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.171

Intolerance Scores

• loftool: 0.0502
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.470
• hipred: Y
• hipred_score: 0.783
• ghis: 0.696

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.987

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Rbm17

Gene ontology

• Biological process: alternative mRNA splicing, via spliceosome;regulation of alternative mRNA splicing, via spliceosome;mRNA splicing, via spliceosome;DNA repair
• Cellular component: nucleoplasm;spliceosomal complex
• Molecular function: RNA binding;protein binding