RNF24

ring finger protein 24, the group of Ring finger proteins

Basic information

Region (hg38): 20:3927308-4015558

Links

ENSG00000101236 ∙ ∙ OMIM:612489 ∙ HGNC:13779 ∙ Uniprot:Q9Y225 ∙ 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 RNF24 gene.

• Inborn genetic diseases (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF24 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in RNF24

This is a list of pathogenic ClinVar variants found in the RNF24 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-3934069-A-C		not specified	Uncertain significance (Jun 30, 2023)
20-3934100-G-T		not specified	Uncertain significance (Mar 17, 2023)
20-3935039-C-T		not specified	Uncertain significance (Feb 21, 2024)
20-3945215-T-C		not specified	Uncertain significance (Aug 22, 2023)
20-3963950-T-C		not specified	Uncertain significance (Mar 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF24	protein_coding	protein_coding	ENST00000432261	6	88274

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0307	0.929	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	57	86.3	0.660	0.00000425	1113
Missense in Polyphen		23	33.838	0.67972		466
Synonymous	0.773	25	30.4	0.822	0.00000157	292
Loss of Function	1.77	4	10.1	0.397	4.88e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000344	0.0000344
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000478	0.0000462
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in TRPCs intracellular trafficking. {ECO:0000269|PubMed:17850865}.

Recessive Scores

• pRec: 0.0806

Intolerance Scores

• loftool: 0.322
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.0897
• hipred: Y
• hipred_score: 0.530
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf24

Gene ontology

• Cellular component: Golgi membrane;Golgi apparatus;endomembrane system;integral component of membrane
• Molecular function: protein binding;zinc ion binding;ubiquitin protein ligase activity