RBM10

RNA binding motif protein 10, the group of Zinc fingers RANBP2-type |RNA binding motif containing|G-patch domain containing|Spliceosomal A complex

Basic information

Region (hg38): X:47145221-47186813

Links

ENSG00000182872 ∙ NCBI:8241 ∙ OMIM:300080 ∙ HGNC:9896 ∙ Uniprot:P0DW28, P98175 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• TARP syndrome (Strong), mode of inheritance: XLR
• TARP syndrome (Strong), mode of inheritance: XL
• TARP syndrome (Strong), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
TARP syndrome	XL	Cardiovascular	The condition can include congenital cardiac anomalies, and awareness may allow early identification and management	Cardiovascular; Craniofacial; Musculoskeletal	5410571; 20451169; 21910224; 24259342; 30189253

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RBM10 gene.

• not provided (7 variants)
• TARP syndrome (6 variants)
• Inborn genetic diseases (2 variants)
• Neurodevelopmental delay (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBM10 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			3	43	15	61
missense		3	77	10	7	97
nonsense	4	2				6
start loss						0
frameshift	8	3	1			12
inframe indel			4		1	5
splice donor/acceptor (+/-2bp)	2	6				8
splice region	1	1	4	9	5	20
non coding				23	15	38
Total	14	14	85	76	38

Variants in RBM10

This is a list of pathogenic ClinVar variants found in the RBM10 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-47145439-C-T			Likely benign (Oct 07, 2019)
X-47145462-T-C		RBM10-related disorder	Benign (Jul 10, 2018)
X-47147429-G-A			Uncertain significance (Nov 03, 2021)
X-47147448-G-T			Uncertain significance (Oct 03, 2023)
X-47147489-A-G			Uncertain significance (Aug 15, 2022)
X-47147501-G-A			Benign (Nov 08, 2023)
X-47147513-C-T			Benign (Feb 27, 2023)
X-47147662-C-CCTGTGCT			Benign (Jul 14, 2018)
X-47169344-A-G			Uncertain significance (Apr 27, 2021)
X-47169363-G-T			Likely benign (May 24, 2023)
X-47169394-G-A			Uncertain significance (Dec 30, 2023)
X-47169411-CATGGACTACCGTTCAT-C		TARP syndrome	Likely pathogenic (Apr 18, 2019)
X-47169412-A-G		Inborn genetic diseases	Uncertain significance (Nov 15, 2021)
X-47169416-A-ACTAC		TARP syndrome	not provided (-)
X-47169422-G-A			Likely benign (Jul 10, 2023)
X-47169430-C-A		Inborn genetic diseases	Uncertain significance (Jul 27, 2022)
X-47169433-C-T			Uncertain significance (Nov 15, 2022)
X-47169434-G-A		Inborn genetic diseases	Likely benign (Oct 13, 2023)
X-47169435-C-T			Uncertain significance (Mar 20, 2023)
X-47169440-A-C			Uncertain significance (Oct 04, 2023)
X-47169455-GC-G		TARP syndrome	Pathogenic (Nov 17, 2011)
X-47169456-C-G			Likely benign (Nov 27, 2023)
X-47169465-CTA-C			Pathogenic (Jan 27, 2016)
X-47169486-G-T		Inborn genetic diseases	Uncertain significance (Jun 29, 2023)
X-47169495-G-A			Likely benign (Nov 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBM10	protein_coding	protein_coding	ENST00000377604	23	41945

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	9.39e-7	123984	0	1	123985	0.00000403

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.46	172	433	0.397	0.0000397	6004
Missense in Polyphen		46	141.72	0.32458		1901
Synonymous	0.242	176	180	0.977	0.0000171	1791
Loss of Function	5.94	1	43.1	0.0232	0.00000350	618

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)	0.0000124	0.00000895
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in post-transcriptional processing, most probably in mRNA splicing. Binds to RNA homopolymers, with a preference for poly(G) and poly(U) and little for poly(A) (By similarity). May bind to specific miRNA hairpins (PubMed:28431233). {ECO:0000250|UniProtKB:P70501, ECO:0000269|PubMed:18315527, ECO:0000269|PubMed:28431233}.
• Disease: DISEASE: TARP syndrome (TARPS) [MIM:311900]: A disorder characterized by the Robin sequence (micrognathia, glossoptosis and cleft palate), talipes equinovarus and cardiac defects. {ECO:0000269|PubMed:20451169}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.157

Intolerance Scores

• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.76

Haploinsufficiency Scores

• pHI: 0.176
• hipred: Y
• hipred_score: 0.771
• ghis: 0.585

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.687

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rbm10
• Phenotype: normal phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of alternative mRNA splicing, via spliceosome;mRNA processing;biological_process;negative regulation of cell population proliferation;RNA splicing;positive regulation of smooth muscle cell apoptotic process;negative regulation of mRNA splicing, via spliceosome;3'-UTR-mediated mRNA stabilization
• Cellular component: nucleus;nuclear speck;protein-containing complex
• Molecular function: RNA binding;protein binding;miRNA binding;identical protein binding;metal ion binding