RBM47

RNA binding motif protein 47, the group of RNA binding motif containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 4:40423266-40630875

Links

ENSG00000163694 ∙ NCBI:54502 ∙ OMIM:619104 ∙ HGNC:30358 ∙ Uniprot:A0AV96 ∙ 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 RBM47 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBM47 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			41	1		42
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	41	2	2

Variants in RBM47

This is a list of pathogenic ClinVar variants found in the RBM47 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-40425921-C-A		not specified	Uncertain significance (Nov 22, 2023)
4-40425926-G-A		not specified	Uncertain significance (Sep 27, 2022)
4-40425954-G-A		not specified	Uncertain significance (Jun 23, 2023)
4-40425960-C-T		not specified	Uncertain significance (Jun 05, 2023)
4-40425961-C-G		not specified	Uncertain significance (Jun 11, 2024)
4-40426012-G-C		not specified	Uncertain significance (Nov 09, 2021)
4-40426012-G-T		not specified	Uncertain significance (Nov 08, 2021)
4-40426074-C-T			Likely benign (Jul 01, 2024)
4-40426076-T-C		not specified	Uncertain significance (Aug 08, 2022)
4-40426122-A-G		not specified	Uncertain significance (Aug 21, 2023)
4-40426134-T-C		not specified	Uncertain significance (Feb 03, 2022)
4-40432667-G-A		not specified	Uncertain significance (Feb 16, 2023)
4-40432695-C-T		not specified	Uncertain significance (Dec 15, 2022)
4-40432696-GGCGGCTGCGGCC-G			Likely benign (Nov 01, 2022)
4-40432703-G-A		not specified	Uncertain significance (Dec 21, 2022)
4-40432709-G-A		not specified	Uncertain significance (Jan 05, 2022)
4-40432710-C-T		not specified	Uncertain significance (Sep 29, 2023)
4-40432719-C-T		not specified	Uncertain significance (Feb 06, 2023)
4-40432748-A-G		not specified	Uncertain significance (May 27, 2022)
4-40432755-T-C		not specified	Uncertain significance (Oct 12, 2022)
4-40432757-G-T		not specified	Uncertain significance (Apr 13, 2022)
4-40432844-C-G		not specified	Uncertain significance (Sep 16, 2021)
4-40432846-A-G			Benign (Sep 17, 2017)
4-40432847-A-G		not specified	Uncertain significance (Oct 13, 2023)
4-40432847-A-T		not specified	Uncertain significance (Feb 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBM47	protein_coding	protein_coding	ENST00000381793	4	207621

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.985	0.0151	125666	0	79	125745	0.000314

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.59	286	439	0.652	0.0000327	3828
Missense in Polyphen		99	179.98	0.55005		1566
Synonymous	0.853	194	210	0.925	0.0000194	1229
Loss of Function	3.90	2	21.5	0.0928	0.00000118	218

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000994	0.000978
Ashkenazi Jewish	0.0000999	0.0000992
East Asian	0.000548	0.000544
Finnish	0.000234	0.000231
European (Non-Finnish)	0.000374	0.000369
Middle Eastern	0.000548	0.000544
South Asian	0.0000327	0.0000327
Other	0.000330	0.000326

dbNSFP

Source: dbNSFP

• Pathway: TYROBP Causal Network (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.109
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.51

Haploinsufficiency Scores

• pHI: 0.559
• hipred: Y
• hipred_score: 0.673
• ghis: 0.536

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.556

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rbm47
• Phenotype: growth/size/body region phenotype; cellular 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); normal phenotype

Zebrafish Information Network

• Gene name: rbm47
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: hematopoietic progenitor cell differentiation;cytidine to uridine editing
• Cellular component: nucleus
• Molecular function: RNA binding;mRNA binding