RBM39

RNA binding motif protein 39, the group of RNA binding motif containing

Basic information

Region (hg38): 20:35701347-35742312

Previous symbols: [ "RNPC2" ]

Links

ENSG00000131051 ∙ NCBI:9584 ∙ OMIM:604739 ∙ HGNC:15923 ∙ Uniprot:Q14498 ∙ 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 RBM39 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBM39 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in RBM39

This is a list of pathogenic ClinVar variants found in the RBM39 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-35704517-C-T		not specified	Uncertain significance (Apr 27, 2023)
20-35704519-T-C		not specified	Uncertain significance (Oct 03, 2022)
20-35704570-T-C		not specified	Uncertain significance (Sep 22, 2023)
20-35721835-T-C		not specified	Uncertain significance (May 23, 2024)
20-35724691-T-C		not specified	Uncertain significance (Feb 12, 2024)
20-35729327-T-C		not specified	Uncertain significance (Feb 12, 2024)
20-35729484-A-C		not specified	Uncertain significance (Feb 23, 2023)
20-35731990-G-A		not specified	Uncertain significance (Apr 20, 2024)
20-35732013-C-T		not specified	Uncertain significance (Mar 14, 2023)
20-35732019-C-T		not specified	Uncertain significance (Jun 16, 2023)
20-35732031-C-T		not specified	Uncertain significance (May 23, 2023)
20-35739016-T-C		not specified	Uncertain significance (Dec 20, 2023)
20-35740828-T-C		not specified	Uncertain significance (Dec 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBM39	protein_coding	protein_coding	ENST00000253363	16	38704

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000185	125710	0	2	125712	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.26	90	296	0.304	0.0000165	3470
Missense in Polyphen		6	57.271	0.10476		704
Synonymous	0.630	85	92.7	0.917	0.00000463	993
Loss of Function	5.24	3	37.8	0.0795	0.00000268	390

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)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional coactivator for steroid nuclear receptors ESR1/ER-alpha and ESR2/ER-beta, and JUN/AP-1 (By similarity). May be involved in pre-mRNA splicing process. {ECO:0000250}.
• Pathway: mRNA Processing (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.348
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.858
• hipred: Y
• hipred_score: 0.739
• ghis: 0.661

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rbm39
• 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)

Gene ontology

• Biological process: RNA processing;mRNA processing;RNA splicing
• Cellular component: nucleoplasm;microtubule organizing center;microtubule cytoskeleton;nuclear speck;protein-containing complex
• Molecular function: RNA binding;protein binding