RBM14-RBM4

RBM14-RBM4 readthrough

Basic information

Region (hg38): 11:66616626-66646469

Links

ENSG00000248643 ∙ NCBI:100526737 ∙ ∙ HGNC:38840 ∙ ∙ ∙ 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 RBM14-RBM4 gene.

• Inborn genetic diseases (21 variants)
• not provided (2 variants)
• Myoepithelial tumor (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBM14-RBM4 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			20	1		21
Total	0	0	22	2	0

Variants in RBM14-RBM4

This is a list of pathogenic ClinVar variants found in the RBM14-RBM4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-66624391-A-T		not specified	Uncertain significance (Jun 16, 2024)
11-66624396-G-A		not specified	Uncertain significance (Aug 02, 2022)
11-66624421-C-G		not specified	Uncertain significance (Mar 26, 2024)
11-66624440-G-T		not specified	Uncertain significance (Mar 25, 2024)
11-66624459-A-G		not specified	Uncertain significance (Apr 29, 2024)
11-66624473-T-C			Likely benign (Nov 01, 2023)
11-66624498-C-T		not specified	Uncertain significance (Jan 03, 2022)
11-66624499-C-A		not specified	Uncertain significance (Jan 16, 2024)
11-66624523-C-G		not specified	Uncertain significance (Dec 19, 2022)
11-66624529-G-A		not specified	Uncertain significance (Feb 01, 2023)
11-66624603-G-A		not specified	Uncertain significance (Jan 04, 2022)
11-66624658-A-G		not specified	Uncertain significance (Dec 01, 2022)
11-66624676-C-T		not specified	Uncertain significance (Dec 15, 2022)
11-66624699-G-A		not specified	Uncertain significance (Jun 10, 2024)
11-66624769-C-G		not specified	Uncertain significance (Mar 28, 2023)
11-66624772-C-T		not specified	Uncertain significance (Nov 09, 2021)
11-66624795-G-A		not specified	Uncertain significance (Mar 07, 2023)
11-66624826-C-G		not specified	Uncertain significance (Mar 17, 2023)
11-66624834-G-A		not specified	Uncertain significance (Sep 12, 2023)
11-66624856-C-T		not specified	Uncertain significance (Oct 05, 2022)
11-66624868-A-G		not specified	Uncertain significance (Apr 30, 2024)
11-66624934-C-T		not specified	Uncertain significance (Nov 10, 2022)
11-66625143-G-A		not specified	Uncertain significance (Mar 07, 2023)
11-66625174-T-C		not specified	Uncertain significance (Apr 26, 2024)
11-66625240-C-G		not specified	Uncertain significance (May 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBM14-RBM4	protein_coding	protein_coding	ENST00000412278	2	29844

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.984	0.0156	124837	0	9	124846	0.0000360

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.98	158	245	0.644	0.0000160	2152
Missense in Polyphen		12	56.325	0.21305		509
Synonymous	-1.30	127	110	1.16	0.00000755	745
Loss of Function	3.29	0	12.6	0.00	6.38e-7	136

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000555	0.0000555
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000353
Middle Eastern	0.0000555	0.0000555
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 1 may function as a nuclear receptor coactivator, enhancing transcription through other coactivators such as NCOA6 and CITED1. Isoform 2, functions as a transcriptional repressor, modulating transcriptional activities of coactivators including isoform 1, NCOA6 and CITED1 (PubMed:11443112). Regulates centriole biogenesis by suppressing the formation of aberrant centriolar protein complexes in the cytoplasm and thus preserving mitotic spindle integrity. Prevents the formation of the STIL-CENPJ complex (which can induce the formation of aberrant centriolar protein complexes) by interfering with the interaction of STIL with CENPJ (PubMed:25385835). Plays a role in the regulation of DNA virus-mediated innate immune response by assembling into the HDP-RNP complex, a complex that serves as a platform for IRF3 phosphorylation and subsequent innate immune response activation through the cGAS-STING pathway (PubMed:28712728). {ECO:0000269|PubMed:11443112, ECO:0000269|PubMed:25385835, ECO:0000269|PubMed:28712728}.
• Pathway: RUNX2 regulates bone development;Transcriptional regulation by RUNX2;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.09

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.380
• ghis: 0.395

Essentials

• essential_gene_CRISPR: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Cellular component: nucleus
• Molecular function: RNA binding