RFPL1

ret finger protein like 1, the group of Ring finger proteins

Basic information

Region (hg38): 22:29438583-29442455

Links

ENSG00000128250 ∙ NCBI:5988 ∙ OMIM:605968 ∙ HGNC:9977 ∙ Uniprot:O75677 ∙ 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 RFPL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RFPL1 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in RFPL1

This is a list of pathogenic ClinVar variants found in the RFPL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-29438916-T-C		not specified	Uncertain significance (Sep 16, 2021)
22-29438943-T-G		not specified	Uncertain significance (Mar 28, 2022)
22-29438958-G-A		not specified	Uncertain significance (May 23, 2023)
22-29438982-T-A		not specified	Uncertain significance (Sep 10, 2024)
22-29438984-A-G		not specified	Uncertain significance (Sep 14, 2022)
22-29439020-C-A		not specified	Uncertain significance (Nov 28, 2023)
22-29439051-A-G		not specified	Uncertain significance (Mar 15, 2024)
22-29439082-G-C		not specified	Uncertain significance (Sep 08, 2024)
22-29439143-C-T		not specified	Uncertain significance (Jan 03, 2024)
22-29441551-C-T		not specified	Uncertain significance (Mar 25, 2024)
22-29441580-C-T		not specified	Uncertain significance (Dec 03, 2021)
22-29441619-T-C		not specified	Uncertain significance (Nov 13, 2024)
22-29441620-G-T		not specified	Uncertain significance (Nov 13, 2024)
22-29441634-C-T		not specified	Likely benign (Nov 27, 2024)
22-29441650-A-C		not specified	Uncertain significance (Mar 01, 2024)
22-29441667-A-G		not specified	Uncertain significance (Mar 18, 2024)
22-29441703-C-T		not specified	Uncertain significance (Apr 12, 2022)
22-29441704-G-A		not specified	Uncertain significance (Feb 06, 2024)
22-29441805-C-T		not specified	Uncertain significance (Dec 27, 2023)
22-29441806-G-A		not specified	Uncertain significance (Dec 16, 2021)
22-29441820-G-A		not specified	Uncertain significance (May 05, 2023)
22-29441841-C-T		not specified	Uncertain significance (Jul 23, 2024)
22-29441890-A-C		not specified	Uncertain significance (Jan 03, 2024)
22-29442006-C-A		not specified	Uncertain significance (Feb 28, 2024)
22-29442015-T-C		not specified	Likely benign (Dec 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RFPL1	protein_coding	protein_coding	ENST00000354373	2	3873

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0124	0.667	125738	0	9	125747	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.409	167	183	0.915	0.0000105	2086
Missense in Polyphen		40	48.734	0.82077		643
Synonymous	-1.47	88	72.2	1.22	0.00000431	638
Loss of Function	0.515	3	4.13	0.726	1.77e-7	58

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000124	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negatively regulates the G2-M phase transition, possibly by promoting cyclin B1/CCNB1 and CDK1 proteasomal degradation and thereby preventing their accumulation during interphase. {ECO:0000269|PubMed:20725088}.

Intolerance Scores

• loftool: 0.915
• rvis_EVS: 1.4
• rvis_percentile_EVS: 94.7

Haploinsufficiency Scores

• pHI: 0.0982
• hipred: N
• hipred_score: 0.112
• ghis: 0.418

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0503

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Gene ontology

• Biological process: cell cycle;negative regulation of cell population proliferation;negative regulation of G2/M transition of mitotic cell cycle;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;positive regulation of apoptotic process;negative regulation of mitotic cell cycle;negative regulation of cell division;positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis
• Cellular component: nucleus;cytoplasm
• Molecular function: metal ion binding