RBM38

RNA binding motif protein 38, the group of RNA binding motif containing

Basic information

Region (hg38): 20:57391396-57409333

Previous symbols: [ "RNPC1" ]

Links

ENSG00000132819 ∙ NCBI:55544 ∙ OMIM:612428 ∙ HGNC:15818 ∙ Uniprot:Q9H0Z9 ∙ 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 RBM38 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBM38 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			13	1	1	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	2

Variants in RBM38

This is a list of pathogenic ClinVar variants found in the RBM38 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-57391604-G-A		not specified	Uncertain significance (Dec 28, 2022)
20-57391630-C-T		not specified	Uncertain significance (Apr 26, 2023)
20-57391634-T-C		not specified	Likely benign (Feb 06, 2023)
20-57391643-C-T			Benign (May 15, 2018)
20-57391685-A-G		not specified	Uncertain significance (Sep 10, 2024)
20-57391739-A-G		not specified	Uncertain significance (Jan 19, 2024)
20-57392685-G-A		not specified	Uncertain significance (Jul 31, 2024)
20-57392686-G-T		not specified	Uncertain significance (Nov 28, 2024)
20-57392726-G-A		not specified	Uncertain significance (Feb 20, 2025)
20-57392736-A-G		not specified	Uncertain significance (Jan 19, 2024)
20-57393287-A-G		not specified	Likely benign (Dec 23, 2024)
20-57393305-C-T		not specified	Uncertain significance (Dec 14, 2022)
20-57407568-C-T		not specified	Uncertain significance (Mar 11, 2025)
20-57407636-T-G		not specified	Uncertain significance (Feb 27, 2023)
20-57407639-G-A			Benign (May 15, 2018)
20-57407674-C-T		not specified	Uncertain significance (Jun 28, 2024)
20-57407691-C-G		not specified	Uncertain significance (Feb 12, 2024)
20-57407707-C-T		not specified	Uncertain significance (Feb 08, 2025)
20-57407740-A-G		not specified	Uncertain significance (Dec 26, 2023)
20-57407782-C-G		not specified	Uncertain significance (Feb 20, 2025)
20-57407794-C-G		not specified	Uncertain significance (Mar 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBM38	protein_coding	protein_coding	ENST00000356208	4	17927

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.716	0.281	124518	0	2	124520	0.00000803

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	113	148	0.762	0.00000985	1492
Missense in Polyphen		17	44.627	0.38094		438
Synonymous	0.0297	72	72.3	0.996	0.00000574	510
Loss of Function	2.38	1	8.46	0.118	3.72e-7	97

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)	0.0000178	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein that specifically bind the 3'-UTR of CDKN1A transcripts, leading to maintain the stability of CDKN1A transcripts, thereby acting as a mediator of the p53/TP53 family to regulate CDKN1A. CDKN1A is a cyclin-dependent kinase inhibitor transcriptionally regulated by the p53/TP53 family to induce cell cycle arrest. Isoform 1, but not isoform 2, has the ability to induce cell cycle arrest in G1 and maintain the stability of CDKN1A transcripts induced by p53/TP53. Also acts as a mRNA splicing factor. Specifically regulates the expression of FGFR2- IIIb, an epithelial cell-specific isoform of FGFR2. Plays a role in myogenic differentiation. {ECO:0000269|PubMed:17050675, ECO:0000269|PubMed:19285943}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.57

Haploinsufficiency Scores

• pHI: 0.160
• hipred: Y
• hipred_score: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.842

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rbm38
• Phenotype: skeleton phenotype; immune system phenotype; neoplasm; 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); hematopoietic system phenotype; liver/biliary system phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: mRNA processing;cell cycle;RNA splicing;regulation of myotube differentiation;cell differentiation;regulation of RNA splicing;3'-UTR-mediated mRNA stabilization
• Cellular component: nucleus;cytosol;ribonucleoprotein complex
• Molecular function: RNA binding;mRNA binding;mRNA 3'-UTR binding