RFPL3S

RFPL3 antisense, the group of Long non-coding RNAs with non-systematic symbols

Basic information

Region (hg38): 22:32359886-32382106

Previous symbols: [ "RFPL3-AS1" ]

Links

ENSG00000205853 ∙ NCBI:10737 ∙ OMIM:605971 ∙ HGNC:9981 ∙ Uniprot:P0C7P2 ∙ 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 RFPL3S gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RFPL3S 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			24	3		27
Total	0	0	24	3	0

Variants in RFPL3S

This is a list of pathogenic ClinVar variants found in the RFPL3S region.

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

Position	Type	Phenotype	Significance	ClinVar
22-32360257-A-G		not specified	Uncertain significance (Feb 15, 2023)
22-32360276-C-G		not specified	Uncertain significance (Jun 03, 2022)
22-32360291-T-C		not specified	Uncertain significance (Sep 02, 2024)
22-32360294-T-C		not specified	Uncertain significance (Jul 16, 2024)
22-32360307-C-A		not specified	Uncertain significance (Dec 03, 2024)
22-32360318-T-C		not specified	Uncertain significance (Oct 08, 2024)
22-32360350-G-T		not specified	Uncertain significance (Aug 17, 2021)
22-32360359-G-A		not specified	Uncertain significance (Nov 15, 2021)
22-32360369-A-G		not specified	Uncertain significance (Feb 08, 2025)
22-32360371-G-A		not specified	Uncertain significance (Jul 31, 2024)
22-32360377-G-A		not specified	Likely benign (May 05, 2022)
22-32360399-G-A		not specified	Uncertain significance (Feb 06, 2023)
22-32360446-A-G		not specified	Uncertain significance (Jul 02, 2024)
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)
22-32360572-C-T		not specified	Uncertain significance (May 11, 2022)
22-32360596-C-T		not specified	Uncertain significance (Sep 01, 2021)
22-32360599-A-G		not specified	Uncertain significance (Jun 17, 2024)
22-32360600-A-G		not specified	Uncertain significance (Aug 14, 2023)
22-32360654-T-C		not specified	Uncertain significance (Sep 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RFPL3S	protein_coding	protein_coding	ENST00000400234	5	22147

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0878	0.774	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.520	38	48.1	0.789	0.00000247	624
Missense in Polyphen		2	2.8835	0.6936		34
Synonymous	0.395	14	16.0	0.874	7.61e-7	180
Loss of Function	1.11	2	4.55	0.440	1.92e-7	64

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: 0.0543
• hipred: N
• hipred_score: 0.146
• ghis: 0.455

Gene Damage Prediction

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