RFPL4A

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

Basic information

Region (hg38): 19:55759097-55763421

Previous symbols: [ "RFPL4" ]

Links

ENSG00000223638 ∙ NCBI:342931 ∙ OMIM:612601 ∙ HGNC:16449 ∙ Uniprot:A6NLU0 ∙ 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 RFPL4A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RFPL4A 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			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	2	0

Variants in RFPL4A

This is a list of pathogenic ClinVar variants found in the RFPL4A region.

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

Position	Type	Phenotype	Significance	ClinVar
19-55761843-C-G		not specified	Uncertain significance (Nov 09, 2024)
19-55761907-A-G		not specified	Uncertain significance (Oct 21, 2024)
19-55761996-A-G		not specified	Uncertain significance (Jan 18, 2025)
19-55762006-C-T		not specified	Uncertain significance (Nov 08, 2022)
19-55762048-C-G		not specified	Uncertain significance (Jan 23, 2023)
19-55762605-G-A		not specified	Uncertain significance (Oct 11, 2024)
19-55762699-C-A		not specified	Uncertain significance (Feb 25, 2025)
19-55762703-C-A		not specified	Uncertain significance (Oct 26, 2021)
19-55762703-C-T		not specified	Uncertain significance (Aug 23, 2021)
19-55762739-C-A		not specified	Uncertain significance (Jul 15, 2021)
19-55762760-G-A		not specified	Uncertain significance (Oct 26, 2024)
19-55762763-A-G		not specified	Uncertain significance (Nov 10, 2024)
19-55762777-G-A		not specified	Uncertain significance (Mar 15, 2024)
19-55762780-G-A		not specified	Uncertain significance (Nov 28, 2024)
19-55762802-A-G		not specified	Uncertain significance (Aug 17, 2022)
19-55762838-G-A		not specified	Uncertain significance (Nov 09, 2024)
19-55762844-T-C		not specified	Uncertain significance (Sep 30, 2024)
19-55762880-G-T		not specified	Uncertain significance (Feb 25, 2025)
19-55763018-G-A		not specified	Uncertain significance (Jan 24, 2025)
19-55763053-G-C		not specified	Uncertain significance (Dec 06, 2024)
19-55763074-G-C		not specified	Uncertain significance (Jan 18, 2025)
19-55763083-C-T		not specified	Uncertain significance (Apr 26, 2024)
19-55763115-T-C			Likely benign (Nov 01, 2024)
19-55763146-A-G		not specified	Uncertain significance (Dec 23, 2024)
19-55763152-C-A		not specified	Uncertain significance (Jul 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RFPL4A	protein_coding	protein_coding	ENST00000434937	2	4162

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0429	0.678	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	94	138	0.682	0.00000681	1779
Missense in Polyphen		29	38.323	0.75672		542
Synonymous	1.13	44	54.6	0.806	0.00000286	529
Loss of Function	0.530	2	2.99	0.669	1.24e-7	49

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.0455
• hipred: N
• hipred_score: 0.112
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0804

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rfpl4

Gene ontology

• Cellular component: nucleus;cytoplasm
• Molecular function: metal ion binding