RFPL4B

ret finger protein like 4B, the group of Ring finger proteins

Basic information

Region (hg38): 6:112347330-112351294

Links

ENSG00000251258 ∙ NCBI:442247 ∙ ∙ HGNC:33264 ∙ Uniprot:Q6ZWI9 ∙ 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 RFPL4B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RFPL4B 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			21	1		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	21	1	0

Variants in RFPL4B

This is a list of pathogenic ClinVar variants found in the RFPL4B region.

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

Position	Type	Phenotype	Significance	ClinVar
6-112349725-A-C		not specified	Uncertain significance (Mar 29, 2023)
6-112349745-G-A		not specified	Likely benign (May 18, 2023)
6-112349775-T-G		not specified	Uncertain significance (Jul 27, 2021)
6-112349792-C-A		not specified	Uncertain significance (Jan 12, 2024)
6-112349793-G-A		not specified	Uncertain significance (Oct 04, 2022)
6-112349806-A-G		not specified	Uncertain significance (Apr 13, 2022)
6-112349840-T-G		not specified	Uncertain significance (Dec 06, 2021)
6-112349887-C-T		not specified	Uncertain significance (Apr 18, 2023)
6-112349900-G-T		not specified	Uncertain significance (Nov 17, 2022)
6-112349923-T-C		not specified	Uncertain significance (Nov 02, 2023)
6-112349944-G-A		not specified	Uncertain significance (Jun 18, 2021)
6-112349994-G-C		not specified	Uncertain significance (Apr 07, 2022)
6-112350007-A-C		not specified	Uncertain significance (Jul 20, 2021)
6-112350057-G-A		not specified	Uncertain significance (May 01, 2024)
6-112350138-G-A		not specified	Uncertain significance (Mar 21, 2024)
6-112350205-C-T		not specified	Uncertain significance (Aug 17, 2022)
6-112350210-G-T		not specified	Uncertain significance (Mar 15, 2024)
6-112350221-C-A		not specified	Uncertain significance (Jun 17, 2022)
6-112350241-A-G		not specified	Uncertain significance (Dec 13, 2022)
6-112350259-T-C		not specified	Uncertain significance (Jan 19, 2022)
6-112350321-C-T		not specified	Uncertain significance (Aug 03, 2022)
6-112350322-G-A		not specified	Uncertain significance (May 07, 2024)
6-112350349-A-T		not specified	Uncertain significance (May 17, 2023)
6-112350442-T-A		not specified	Uncertain significance (Feb 22, 2023)
6-112350471-A-T		not specified	Uncertain significance (May 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RFPL4B	protein_coding	protein_coding	ENST00000441065	1	3967

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.264	139	148	0.939	0.00000869	1744
Missense in Polyphen		31	34.658	0.89446		469
Synonymous	0.0386	59	59.4	0.994	0.00000368	520
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.564
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.53

Haploinsufficiency Scores

• pHI: 0.00674
• hipred: N
• hipred_score: 0.112
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• 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

Mouse Genome Informatics

• Gene name: Rfpl4b

Gene ontology

• Molecular function: metal ion binding