RFPL3

ret finger protein like 3, the group of Ring finger proteins

Basic information

Region (hg38): 22:32354885-32361161

Links

ENSG00000128276 ∙ NCBI:10738 ∙ OMIM:605970 ∙ HGNC:9980 ∙ Uniprot:O75679 ∙ 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 RFPL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RFPL3 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			28	3		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	3	0

Variants in RFPL3

This is a list of pathogenic ClinVar variants found in the RFPL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-32358080-G-T		not specified	Uncertain significance (Jul 13, 2022)
22-32358104-G-C		not specified	Uncertain significance (Aug 11, 2022)
22-32358168-C-G		not specified	Uncertain significance (Apr 25, 2022)
22-32358174-C-A		not specified	Uncertain significance (May 03, 2023)
22-32358220-C-G		not specified	Uncertain significance (Sep 17, 2021)
22-32358246-G-A		not specified	Uncertain significance (Feb 27, 2023)
22-32358287-T-G		not specified	Uncertain significance (Apr 04, 2023)
22-32358291-G-A		not specified	Uncertain significance (Nov 17, 2023)
22-32358318-A-G		not specified	Uncertain significance (Mar 20, 2023)
22-32358352-G-A		not specified	Uncertain significance (Mar 01, 2024)
22-32358392-G-C		not specified	Uncertain significance (Aug 01, 2022)
22-32358429-A-T		not specified	Uncertain significance (Jun 30, 2022)
22-32360257-A-G		not specified	Uncertain significance (Feb 15, 2023)
22-32360276-C-G		not specified	Uncertain significance (Jun 03, 2022)
22-32360350-G-T		not specified	Uncertain significance (Aug 17, 2021)
22-32360359-G-A		not specified	Uncertain significance (Nov 15, 2021)
22-32360377-G-A		not specified	Likely benign (May 05, 2022)
22-32360399-G-A		not specified	Uncertain significance (Feb 06, 2023)
22-32360485-T-C		not specified	Likely benign (Jul 07, 2022)
22-32360540-G-C		not specified	Uncertain significance (Jun 18, 2021)
22-32360548-A-G		not specified	Likely benign (May 31, 2023)
22-32360551-C-T		not specified	Uncertain significance (Feb 13, 2024)
22-32360564-G-C		not specified	Uncertain significance (Feb 14, 2024)
22-32360567-C-G		not specified	Uncertain significance (Jul 19, 2022)
22-32360567-C-T		not specified	Uncertain significance (Apr 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RFPL3	protein_coding	protein_coding	ENST00000249007	2	6277

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000166	0.144	125676	0	72	125748	0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.435	198	182	1.09	0.0000106	2062
Missense in Polyphen		54	51.331	1.052		662
Synonymous	-1.37	87	72.2	1.20	0.00000431	641
Loss of Function	-1.07	6	3.75	1.60	1.58e-7	55

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00215	0.00214
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.000163	0.000163
Finnish	0.000231	0.000231
European (Non-Finnish)	0.0000967	0.0000967
Middle Eastern	0.000163	0.000163
South Asian	0.0000989	0.0000980
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: (Microbial infection) Stimulates the activity of Human Immunodeficiency Virus 1/HIV-1 pre-integration complex. {ECO:0000269|PubMed:25107902}.

Intolerance Scores

• loftool: 0.828
• rvis_EVS: 0.69
• rvis_percentile_EVS: 85.18

Haploinsufficiency Scores

• pHI: 0.0432
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000120

Gene Damage Prediction

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

Gene ontology

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