RTF2

replication termination factor 2

Basic information

Region (hg38): 20:56468585-56519449

Previous symbols: [ "C20orf43", "RTFDC1" ]

Links

ENSG00000022277 ∙ NCBI:51507 ∙ ∙ HGNC:15890 ∙ Uniprot:Q9BY42 ∙ 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 RTF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTF2 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			25
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	0	0

Variants in RTF2

This is a list of pathogenic ClinVar variants found in the RTF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-56468722-C-A		not specified	Uncertain significance (Aug 13, 2021)
20-56468723-C-T		not specified	Uncertain significance (Jan 23, 2024)
20-56468764-A-G		not specified	Uncertain significance (Sep 23, 2023)
20-56473304-G-A		not specified	Uncertain significance (Oct 20, 2021)
20-56474719-A-C		not specified	Uncertain significance (May 03, 2023)
20-56474727-G-C		not specified	Uncertain significance (Nov 14, 2023)
20-56477034-A-G		not specified	Uncertain significance (Feb 28, 2023)
20-56477055-A-G		not specified	Uncertain significance (Apr 12, 2023)
20-56477078-C-T		not specified	Uncertain significance (Oct 04, 2022)
20-56477093-G-A		not specified	Uncertain significance (Oct 04, 2022)
20-56477115-G-T		not specified	Uncertain significance (Feb 06, 2024)
20-56484116-G-T		not specified	Uncertain significance (Mar 02, 2023)
20-56484131-G-A		not specified	Uncertain significance (Jan 22, 2024)
20-56484133-G-A		not specified	Uncertain significance (Dec 06, 2022)
20-56513339-G-A		not specified	Uncertain significance (Jun 28, 2022)
20-56513355-A-G		not specified	Uncertain significance (Sep 15, 2021)
20-56513378-G-A		not specified	Uncertain significance (Jan 04, 2022)
20-56513390-A-G		not specified	Uncertain significance (May 13, 2024)
20-56516948-C-T		not specified	Uncertain significance (Aug 17, 2021)
20-56516977-G-T		not specified	Uncertain significance (Jan 04, 2024)
20-56516985-T-A		not specified	Uncertain significance (Mar 29, 2022)
20-56517133-C-T		not specified	Uncertain significance (Aug 17, 2022)
20-56517185-G-C		not specified	Uncertain significance (Jun 16, 2024)
20-56518145-G-T		not specified	Uncertain significance (Apr 25, 2022)
20-56518152-G-A		not specified	Uncertain significance (Jun 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RTF2	protein_coding	protein_coding	ENST00000023939	9	50297

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000643	0.980	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	124	173	0.718	0.00000958	2005
Missense in Polyphen		36	76.492	0.47064		905
Synonymous	1.09	53	64.1	0.826	0.00000371	565
Loss of Function	2.06	8	17.2	0.464	9.90e-7	212

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000200	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.000243	0.000231
European (Non-Finnish)	0.0000806	0.0000791
Middle Eastern	0.0000546	0.0000544
South Asian	0.00	0.00
Other	0.000333	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0923

Intolerance Scores

• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.0931
• hipred: N
• hipred_score: 0.229
• ghis: 0.664

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Rtf2