RNF13

ring finger protein 13, the group of Ring finger proteins

Basic information

Region (hg38): 3:149812769-149962139

Links

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

Phenotypes

GenCC

Source: genCC

• developmental and epileptic encephalopathy, 73 (Limited), 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.

• not provided (143 variants)
• Developmental and epileptic encephalopathy, 73 (10 variants)
• Inborn genetic diseases (7 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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	18	4	23
missense	2		74	7	2	85
nonsense	1	2	4			7
start loss						0
frameshift		2	3			5
inframe indel			2			2
splice variant			3	12	2	17
non coding			2	11	2	15
Total	3	4	89	48	10

Variants in RNF13

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

Position	Type	Phenotype	Significance	ClinVar
3-149846042-G-A			Uncertain significance (Aug 26, 2021)
3-149846060-G-A			Uncertain significance (Jun 22, 2021)
3-149846069-G-A			Uncertain significance (Oct 18, 2022)
3-149846070-T-A			Uncertain significance (May 17, 2022)
3-149846072-T-C			Uncertain significance (Mar 29, 2023)
3-149846078-A-G			Uncertain significance (Oct 13, 2022)
3-149846083-G-T			Uncertain significance (Aug 27, 2021)
3-149846111-C-A			Uncertain significance (Aug 31, 2021)
3-149846115-T-A		Inborn genetic diseases	Uncertain significance (Jun 09, 2022)
3-149846125-A-G			Likely benign (Sep 27, 2022)
3-149846132-A-G		Developmental and epileptic encephalopathy, 73	Uncertain significance (-)
3-149846149-A-G			Likely benign (Sep 06, 2022)
3-149846158-T-C			Likely benign (Mar 25, 2021)
3-149872014-C-T			Likely benign (Sep 15, 2022)
3-149872032-T-G			Uncertain significance (Sep 27, 2022)
3-149872045-CAA-C			Uncertain significance (Jul 12, 2022)
3-149872049-A-G			Likely benign (Oct 24, 2022)
3-149872051-C-A			Uncertain significance (Jul 12, 2022)
3-149872066-A-AGGC			Uncertain significance (Oct 13, 2022)
3-149872071-A-G			Uncertain significance (Feb 14, 2022)
3-149872086-G-A			Uncertain significance (Sep 24, 2021)
3-149872095-A-T		Developmental and epileptic encephalopathy, 73	Uncertain significance (May 06, 2021)
3-149872100-A-G			Likely benign (Aug 16, 2022)
3-149872107-A-T		Inborn genetic diseases	Uncertain significance (Jan 10, 2023)
3-149872115-C-T			Likely benign (Aug 01, 2023)

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