RBM42

RNA binding motif protein 42, the group of RNA binding motif containing|tri-snRP complex

Basic information

Region (hg38): 19:35629030-35637686

Links

ENSG00000126254 ∙ NCBI:79171 ∙ OMIM:613232 ∙ HGNC:28117 ∙ Uniprot:Q9BTD8 ∙ 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 RBM42 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBM42 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in RBM42

This is a list of pathogenic ClinVar variants found in the RBM42 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-35629185-C-T		not specified	Uncertain significance (Apr 25, 2022)
19-35629606-T-A		not specified	Uncertain significance (Dec 03, 2021)
19-35631194-A-G		not specified	Uncertain significance (Mar 06, 2023)
19-35631365-C-G		not specified	Uncertain significance (Feb 22, 2024)
19-35631379-G-A		not specified	Uncertain significance (Apr 07, 2023)
19-35632966-G-A		not specified	Uncertain significance (Mar 18, 2024)
19-35633085-C-G		not specified	Uncertain significance (Feb 26, 2024)
19-35633103-G-A		not specified	Uncertain significance (Oct 03, 2023)
19-35633109-C-A		not specified	Uncertain significance (Jun 24, 2022)
19-35633109-C-T		not specified	Uncertain significance (Feb 14, 2023)
19-35633112-C-A		not specified	Uncertain significance (Mar 20, 2024)
19-35633203-G-A		not specified	Uncertain significance (Jan 03, 2024)
19-35633217-C-A		not specified	Uncertain significance (Aug 17, 2022)
19-35633720-G-C		not specified	Uncertain significance (Aug 03, 2022)
19-35633763-C-T		not specified	Uncertain significance (Apr 06, 2024)
19-35633766-C-T		not specified	Uncertain significance (Sep 27, 2021)
19-35633793-C-T		not specified	Uncertain significance (Apr 07, 2023)
19-35633804-G-A		not specified	Uncertain significance (Mar 29, 2023)
19-35633886-C-T		not specified	Uncertain significance (Nov 10, 2022)
19-35633985-G-A		not specified	Uncertain significance (Oct 03, 2022)
19-35634014-C-G		not specified	Uncertain significance (Apr 18, 2023)
19-35634268-C-A		not specified	Uncertain significance (Dec 07, 2021)
19-35637187-G-A		not specified	Uncertain significance (Dec 06, 2022)
19-35637220-G-A		not specified	Uncertain significance (Feb 06, 2024)
19-35637301-G-A		not specified	Uncertain significance (Feb 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBM42	protein_coding	protein_coding	ENST00000262633	10	8657

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.748	0.252	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.39	184	300	0.613	0.0000194	3003
Missense in Polyphen		35	61.533	0.5688		592
Synonymous	1.62	94	116	0.808	0.00000707	1091
Loss of Function	3.24	3	17.7	0.170	9.58e-7	202

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000629	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds (via the RRM domain) to the 3'-untranslated region (UTR) of CDKN1A mRNA. {ECO:0000250}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.257
• rvis_EVS: -0.29
• rvis_percentile_EVS: 32.94

Haploinsufficiency Scores

• pHI: 0.204
• hipred: Y
• hipred_score: 0.704
• ghis: 0.614

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.960

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rbm42

Zebrafish Information Network

• Gene name: rbm42
• Affected structure: anatomical system
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: negative regulation of mRNA splicing, via spliceosome
• Cellular component: nucleus;cytoplasm;ribonucleoprotein complex
• Molecular function: RNA binding;protein binding