RFPL2

ret finger protein like 2, the group of Ring finger proteins

Basic information

Region (hg38): 22:32190435-32205073

Links

ENSG00000128253 ∙ NCBI:10739 ∙ OMIM:605969 ∙ HGNC:9979 ∙ Uniprot:O75678 ∙ 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 RFPL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RFPL2 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			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	0

Variants in RFPL2

This is a list of pathogenic ClinVar variants found in the RFPL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-32190792-G-A		not specified	Uncertain significance (Dec 02, 2022)
22-32190813-C-T		not specified	Uncertain significance (May 06, 2024)
22-32190842-A-G		not specified	Uncertain significance (Feb 23, 2023)
22-32190845-C-A		not specified	Uncertain significance (Aug 12, 2021)
22-32190861-G-A		not specified	Uncertain significance (Feb 14, 2024)
22-32190978-C-A		not specified	Uncertain significance (Jan 23, 2024)
22-32191014-C-G		not specified	Uncertain significance (Apr 04, 2023)
22-32191021-G-T		not specified	Uncertain significance (Aug 12, 2021)
22-32191031-G-A		not specified	Uncertain significance (Sep 01, 2021)
22-32191118-C-T		not specified	Uncertain significance (Apr 13, 2022)
22-32191125-C-G		not specified	Uncertain significance (Dec 21, 2022)
22-32191128-A-T		not specified	Uncertain significance (Aug 09, 2021)
22-32191139-A-G		not specified	Uncertain significance (Jun 07, 2024)
22-32191167-C-T		not specified	Uncertain significance (May 17, 2023)
22-32191259-C-T		not specified	Uncertain significance (May 20, 2024)
22-32191283-C-T		not specified	Uncertain significance (Jul 06, 2021)
22-32191332-T-G		not specified	Uncertain significance (Jun 22, 2024)
22-32192913-C-T		not specified	Uncertain significance (May 23, 2024)
22-32192964-T-C		not specified	Uncertain significance (Jan 26, 2022)
22-32193000-C-A		not specified	Uncertain significance (Aug 28, 2023)
22-32193000-C-T		not specified	Uncertain significance (Jan 10, 2023)
22-32193028-T-C		not specified	Uncertain significance (May 08, 2024)
22-32193033-G-C		not specified	Likely benign (Oct 05, 2023)
22-32193055-C-T		not specified	Uncertain significance (Mar 25, 2024)
22-32193100-C-T		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RFPL2	protein_coding	protein_coding	ENST00000400237	4	14297

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.54e-7	0.109	125519	2	227	125748	0.000911

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00517	222	222	0.999	0.0000128	2460
Missense in Polyphen		55	60.581	0.90787		782
Synonymous	-0.788	94	84.8	1.11	0.00000498	758
Loss of Function	-0.525	9	7.45	1.21	3.14e-7	98

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000923	0.000877
Ashkenazi Jewish	0.0113	0.0108
East Asian	0.000571	0.000544
Finnish	0.0000468	0.0000462
European (Non-Finnish)	0.000574	0.000563
Middle Eastern	0.000571	0.000544
South Asian	0.000603	0.000555
Other	0.00101	0.000978

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.915
• rvis_EVS: 1.35
• rvis_percentile_EVS: 94.4

Haploinsufficiency Scores

• pHI: 0.0320
• hipred: N
• hipred_score: 0.172
• ghis: 0.410

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0301

Gene Damage Prediction

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

Gene ontology

• Molecular function: metal ion binding