RLF

RLF zinc finger, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 1:40161387-40240921

Links

ENSG00000117000 ∙ NCBI:6018 ∙ OMIM:180610 ∙ HGNC:10025 ∙ Uniprot:Q13129 ∙ 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 RLF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RLF 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				2	3	5
missense			97	4	3	104
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	97	6	6

Variants in RLF

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

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

Position	Type	Phenotype	Significance	ClinVar
1-40161409-G-A		not specified	Uncertain significance (Dec 14, 2022)
1-40161412-A-G		not specified	Uncertain significance (Aug 08, 2022)
1-40161420-C-G		not specified	Uncertain significance (Mar 01, 2023)
1-40161422-C-T		not specified	Uncertain significance (Nov 09, 2021)
1-40161427-G-A		not specified	Uncertain significance (Oct 05, 2023)
1-40161432-C-A			Likely benign (Dec 01, 2024)
1-40161436-G-C		not specified	Uncertain significance (Mar 23, 2022)
1-40161455-C-T		not specified	Uncertain significance (May 20, 2024)
1-40161476-A-G		not specified	Uncertain significance (Dec 21, 2022)
1-40161488-C-T		not specified	Uncertain significance (Sep 29, 2023)
1-40161588-A-C		not specified	Uncertain significance (Aug 19, 2021)
1-40161590-A-T		not specified	Uncertain significance (Oct 26, 2022)
1-40189098-T-C		not specified	Uncertain significance (Aug 01, 2024)
1-40202468-T-A		not specified	Uncertain significance (Jul 12, 2023)
1-40202498-A-G		not specified	Uncertain significance (Apr 13, 2023)
1-40202501-G-A		not specified	Uncertain significance (Aug 27, 2024)
1-40202562-C-G		not specified	Uncertain significance (Apr 20, 2024)
1-40202572-A-G			Benign (Apr 04, 2018)
1-40202583-C-G			Benign (Mar 29, 2018)
1-40231591-G-A		not specified	Uncertain significance (Nov 09, 2024)
1-40231605-A-G		not specified	Uncertain significance (Aug 02, 2021)
1-40231648-T-C		not specified	Uncertain significance (Jun 24, 2022)
1-40235819-A-G		not specified	Uncertain significance (Oct 25, 2024)
1-40235958-T-C		not specified	Uncertain significance (Apr 06, 2022)
1-40236014-C-G		not specified	Uncertain significance (Sep 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RLF	protein_coding	protein_coding	ENST00000372771	8	79549

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	2.28e-12	125122	0	1	125123	0.00000400

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.46	669	973	0.688	0.0000471	12682
Missense in Polyphen		107	321.14	0.33319		4151
Synonymous	-0.225	358	353	1.02	0.0000167	3482
Loss of Function	7.93	0	73.2	0.00	0.00000402	1024

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000619	0.0000619
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

• Function: FUNCTION: May be involved in transcriptional regulation.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.00696
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.19

Haploinsufficiency Scores

• pHI: 0.537
• hipred: Y
• hipred_score: 0.725
• ghis: 0.493

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.941

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rlf
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region phenotype

Gene ontology

• Biological process: regulation of transcription, DNA-templated;DNA integration;regulation of DNA methylation;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;chromosome organization;histone H3-K4 monomethylation
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;zinc ion binding