RNF13

ring finger protein 13, the group of Ring finger proteins

Basic information

Region (hg38): 3:149812770-149962139

Links

ENSG00000082996 ∙ NCBI:11342 ∙ OMIM:609247 ∙ HGNC:10057 ∙ Uniprot:O43567 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• developmental and epileptic encephalopathy, 73 (Limited), mode of inheritance: AD
• developmental and epileptic encephalopathy, 73 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Developmental and epileptic encephalopathy 73	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Audiologic/Otolaryngologic; Craniofacial; Neurologic	30595371

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RNF13 gene.

• Developmental and epileptic encephalopathy, 73 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF13 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				48	2	50
missense			99	5	7	111
nonsense	1	1	3			5
start loss						0
frameshift		2	6			8
inframe indel			2	1		3
splice donor/acceptor (+/-2bp)			2			2
splice region			2	15	3	20
non coding			2	15	2	19
Total	1	3	114	69	11

Variants in RNF13

This is a list of pathogenic ClinVar variants found in the RNF13 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-149846031-T-A			Uncertain significance (Jun 02, 2024)
3-149846041-A-G			Likely benign (Dec 12, 2023)
3-149846042-G-A			Uncertain significance (Feb 16, 2024)
3-149846042-G-C			Likely benign (Jan 06, 2025)
3-149846051-A-G			Uncertain significance (Jan 05, 2023)
3-149846060-G-A			Uncertain significance (Jun 22, 2021)
3-149846065-A-T			Likely benign (Nov 05, 2024)
3-149846067-A-G			Uncertain significance (Nov 24, 2023)
3-149846069-G-A		not specified	Conflicting classifications of pathogenicity (Jan 22, 2025)
3-149846070-T-A			Uncertain significance (Dec 27, 2022)
3-149846072-T-C			Uncertain significance (Mar 29, 2023)
3-149846076-C-T			Uncertain significance (Sep 15, 2023)
3-149846078-A-G			Benign (Oct 15, 2024)
3-149846083-G-T			Uncertain significance (Dec 13, 2023)
3-149846099-G-C		not specified	Uncertain significance (Jan 02, 2025)
3-149846111-C-A			Uncertain significance (Feb 17, 2024)
3-149846115-T-A		not specified	Conflicting classifications of pathogenicity (Aug 13, 2024)
3-149846116-G-A			Likely benign (Dec 30, 2023)
3-149846116-G-C			Likely benign (Jun 04, 2024)
3-149846125-A-G			Likely benign (Feb 02, 2023)
3-149846132-A-G		Developmental and epileptic encephalopathy, 73	Uncertain significance (-)
3-149846145-G-T			Uncertain significance (Dec 23, 2023)
3-149846149-A-G			Likely benign (Sep 06, 2022)
3-149846158-T-C			Likely benign (Oct 21, 2024)
3-149852546-G-A		RNF13-related disorder	Uncertain significance (Jan 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF13	protein_coding	protein_coding	ENST00000344229	9	149432

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000403	0.963	125732	0	12	125744	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.901	158	193	0.818	0.00000919	2506
Missense in Polyphen		39	57.7	0.67591		788
Synonymous	-0.618	77	70.4	1.09	0.00000353	705
Loss of Function	1.86	8	16.0	0.499	6.69e-7	244

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000546	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000677	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase that may play a role in controlling cell proliferation. {ECO:0000269|PubMed:18794910}.

Recessive Scores

• pRec: 0.0875

Intolerance Scores

• loftool: 0.732
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• pHI: 0.397
• hipred: N
• hipred_score: 0.204
• ghis: 0.513

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.866

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf13
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); limbs/digits/tail phenotype; vision/eye phenotype

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein autoubiquitination
• Cellular component: Golgi membrane;nuclear inner membrane;nucleoplasm;lysosomal membrane;endoplasmic reticulum membrane;cytosol;integral component of membrane;late endosome membrane;intracellular membrane-bounded organelle
• Molecular function: ubiquitin-protein transferase activity;protein binding;metal ion binding;ubiquitin protein ligase activity