RNF113A

ring finger protein 113A, the group of Ring finger proteins|Spliceosomal C complex|Spliceosomal Bact complex|Spliceosomal P complex|NTC associated proteins

Basic information

Region (hg38): X:119870475-119871733

Previous symbols: [ "ZNF183" ]

Links

ENSG00000125352 ∙ NCBI:7737 ∙ OMIM:300951 ∙ HGNC:12974 ∙ Uniprot:O15541 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• trichothiodystrophy 5, nonphotosensitive (Limited), mode of inheritance: XL
• trichothiodystrophy (Supportive), mode of inheritance: AR
• trichothiodystrophy 5, nonphotosensitive (Limited), mode of inheritance: XL
• trichothiodystrophy 5, nonphotosensitive (Moderate), mode of inheritance: XL
• trichothiodystrophy 5, nonphotosensitive (Strong), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Trichothiodystrophy 5, nonphotosensitive	XL	Allergy/Immunology/Infectious	The condition can involve recurrent infections, and awareness may allow preventive measures, and early and aggressive treatment of infections	Allergy/Immunology/Infectious; Craniofacial; Dermatologic; Endocrine; Genitourinary; Musculoskeletal; Neurologic	19377476; 25612912; 31130284; 31880405

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RNF113A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF113A 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			8	17	1	26
missense		1	49	5	1	56
nonsense						0
start loss						0
frameshift		1	1			2
inframe indel			2			2
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	2	60	22	3

Variants in RNF113A

This is a list of pathogenic ClinVar variants found in the RNF113A region.

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

Position	Type	Phenotype	Significance	ClinVar
X-119870591-G-A			Likely benign (Dec 15, 2022)
X-119870595-A-C			Uncertain significance (Jun 14, 2022)
X-119870603-C-T			Likely benign (Jul 09, 2022)
X-119870608-C-T			Benign (Jan 29, 2024)
X-119870619-G-A			Uncertain significance (Jun 03, 2023)
X-119870621-C-T		RNF113A-related disorder	Uncertain significance (Nov 24, 2023)
X-119870622-A-C		RNF113A-related disorder	Uncertain significance (Jul 02, 2023)
X-119870638-C-A		not specified	Uncertain significance (Jun 22, 2024)
X-119870639-C-A			Uncertain significance (Sep 15, 2022)
X-119870650-C-T			Uncertain significance (Jan 15, 2022)
X-119870662-C-T		not specified	Uncertain significance (Nov 30, 2022)
X-119870699-G-A			Uncertain significance (Oct 26, 2022)
X-119870703-T-C		not specified	Uncertain significance (Oct 03, 2022)
X-119870703-TTGGTCTGC-T		Trichothiodystrophy 5, nonphotosensitive	Uncertain significance (Feb 15, 2018)
X-119870713-G-A		Trichothiodystrophy 5, nonphotosensitive	Pathogenic (Apr 01, 2015)
X-119870715-T-A			Uncertain significance (Dec 31, 2023)
X-119870715-TCA-T		Trichothiodystrophy 5, nonphotosensitive	Pathogenic (May 08, 2020)
X-119870722-CAT-C		Trichothiodystrophy 5, nonphotosensitive	Likely pathogenic (Sep 01, 2023)
X-119870733-G-A		not specified	Uncertain significance (Dec 06, 2023)
X-119870742-C-T		not specified	Uncertain significance (Aug 14, 2023)
X-119870752-GC-G		Abnormal cerebral morphology	Likely pathogenic (-)
X-119870754-A-G		Trichothiodystrophy 5, nonphotosensitive	Uncertain significance (Apr 18, 2022)
X-119870759-A-G			Likely benign (Oct 20, 2022)
X-119870778-T-C			Likely pathogenic (Mar 24, 2016)
X-119870780-C-T			Likely benign (Jan 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF113A	protein_coding	protein_coding	ENST00000371442	1	1295

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.889	0.110	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.77	77	135	0.571	0.00000897	2285
Missense in Polyphen		5	37.296	0.13406		631
Synonymous	0.721	45	51.6	0.872	0.00000350	646
Loss of Function	2.47	0	7.13	0.00	4.58e-7	132

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
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: E3 ubiquitin-protein ligase that catalyzes the transfer of ubiquitin onto target proteins (PubMed:28978524, PubMed:29144457). Catalyzes polyubiquitination of SNRNP200/BRR2 with non-canonical 'Lys-63'-linked polyubiquitin chains (PubMed:29144457). Plays a role in DNA repair via its role in the synthesis of 'Lys-63'-linked polyubiquitin chains that recruit ALKBH3 and the ASCC complex to sites of DNA damage by alkylating agents (PubMed:29144457). Ubiquitinates CXCR4, leading to its degradation, and thereby contributes to the termination of CXCR4 signaling (PubMed:28978524). {ECO:0000269|PubMed:28978524, ECO:0000269|PubMed:29144457}.

Recessive Scores

• pRec: 0.0928

Intolerance Scores

• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.22

Haploinsufficiency Scores

• pHI: 0.155
• hipred: Y
• hipred_score: 0.592

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf113a1

Zebrafish Information Network

• Gene name: rnf113a
• Affected structure: anatomical system
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: DNA repair;mRNA processing;protein ubiquitination;isopeptide cross-linking via N6-glycyl-L-lysine;snoRNA splicing;negative regulation of chemokine-mediated signaling pathway
• Cellular component: U2-type spliceosomal complex;nuclear speck
• Molecular function: ubiquitin-protein transferase activity;protein binding;metal ion binding