RBM19

RNA binding motif protein 19, the group of RNA binding motif containing|SSU processome

Basic information

Region (hg38): 12:113816737-113966325

Links

ENSG00000122965 ∙ NCBI:9904 ∙ OMIM:616444 ∙ HGNC:29098 ∙ Uniprot:Q9Y4C8 ∙ 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 RBM19 gene.

• Inborn genetic diseases (39 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBM19 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			35	4		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	4	0

Variants in RBM19

This is a list of pathogenic ClinVar variants found in the RBM19 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-113823286-C-T		not specified	Uncertain significance (Dec 06, 2021)
12-113844695-G-A		not specified	Uncertain significance (Jul 27, 2022)
12-113844700-G-C		not specified	Uncertain significance (Mar 07, 2024)
12-113844787-C-T		not specified	Uncertain significance (Dec 22, 2023)
12-113858799-C-G		not specified	Uncertain significance (Mar 29, 2022)
12-113858826-C-T		not specified	Uncertain significance (Aug 02, 2023)
12-113858870-C-T		not specified	Uncertain significance (Jan 27, 2022)
12-113858884-C-G		not specified	Uncertain significance (Jan 17, 2024)
12-113914995-G-C		not specified	Uncertain significance (Sep 27, 2022)
12-113915017-C-T		not specified	Uncertain significance (Dec 17, 2021)
12-113915055-T-G		not specified	Uncertain significance (Aug 12, 2021)
12-113915078-C-T		not specified	Uncertain significance (Nov 02, 2023)
12-113918401-C-T		not specified	Uncertain significance (Dec 15, 2022)
12-113918420-C-G		not specified	Uncertain significance (May 03, 2023)
12-113918441-C-T		not specified	Likely benign (Jun 16, 2023)
12-113920688-C-T		not specified	Uncertain significance (Sep 27, 2021)
12-113927064-T-G		not specified	Likely benign (Jan 10, 2023)
12-113927113-C-G		not specified	Uncertain significance (Jan 31, 2024)
12-113927122-T-C		not specified	Uncertain significance (Jan 04, 2024)
12-113927137-C-T		not specified	Uncertain significance (Dec 27, 2023)
12-113927143-C-T		not specified	Uncertain significance (Aug 09, 2021)
12-113927218-C-T		not specified	Uncertain significance (Dec 18, 2023)
12-113937051-G-A		not specified	Uncertain significance (Feb 01, 2023)
12-113937117-T-G		not specified	Uncertain significance (Sep 15, 2022)
12-113940019-C-A		not specified	Uncertain significance (Dec 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBM19	protein_coding	protein_coding	ENST00000545145	24	149634

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.72e-12	0.999	125620	1	127	125748	0.000509

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.176	583	571	1.02	0.0000346	6307
Missense in Polyphen		187	201.58	0.92767		2044
Synonymous	0.541	234	245	0.956	0.0000168	1823
Loss of Function	3.14	28	52.6	0.532	0.00000267	623

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000940	0.000940
Ashkenazi Jewish	0.00	0.00
East Asian	0.000762	0.000761
Finnish	0.000241	0.000231
European (Non-Finnish)	0.000443	0.000440
Middle Eastern	0.000762	0.000761
South Asian	0.000884	0.000850
Other	0.000659	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in embryo pre-implantation development. {ECO:0000250}.
• Pathway: miR-targeted genes in lymphocytes - TarBase (Consensus)

Recessive Scores

• pRec: 0.168

Intolerance Scores

• loftool: 0.924
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.27

Haploinsufficiency Scores

• pHI: 0.233
• hipred: Y
• hipred_score: 0.528
• ghis: 0.528

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.895

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Rbm19
• Phenotype: embryo 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); cellular phenotype

Zebrafish Information Network

• Gene name: rbm19
• Affected structure: anatomical system
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: regulation of alternative mRNA splicing, via spliceosome;multicellular organism development;positive regulation of embryonic development;mRNA cis splicing, via spliceosome
• Cellular component: nucleoplasm;chromosome;nucleolus;cytoplasm;membrane;nuclear speck
• Molecular function: RNA binding