RNF212

ring finger protein 212, the group of Ring finger proteins

Basic information

Region (hg38): 4:1056249-1113564

Previous symbols: [ "LOC285498" ]

Links

ENSG00000178222 ∙ NCBI:285498 ∙ OMIM:612041 ∙ HGNC:27729 ∙ Uniprot:Q495C1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure 62 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 62	AR	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	Genitourinary	31125047

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RNF212 gene.

• Inborn genetic diseases (11 variants)
• not provided (2 variants)
• not specified (1 variants)
• Non-obstructive azoospermia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF212 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			10		1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		2	3
Total	0	0	11	0	3

Variants in RNF212

This is a list of pathogenic ClinVar variants found in the RNF212 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-1056489-C-G		RNF212-related disorder	Likely benign (Oct 04, 2022)
4-1056828-G-A		RNF212-related disorder	Likely benign (Dec 06, 2022)
4-1056845-C-T		RNF212-related disorder	Likely benign (Oct 13, 2023)
4-1056848-C-T		RNF212-related disorder	Benign (Mar 10, 2022)
4-1056865-G-A		RNF212-related disorder	Benign (Mar 07, 2022)
4-1058283-AGAACGCAGTGAAGAAGGTGCTTGCGGGGG-A		RNF212-related disorder	Likely benign (Feb 09, 2023)
4-1058312-G-A		RNF212-related disorder	Likely benign (Mar 11, 2022)
4-1058337-T-C		RNF212-related disorder	Benign (Mar 07, 2022)
4-1058378-A-C		RNF212-related disorder	Benign (Mar 07, 2022)
4-1073016-T-A		not specified	Uncertain significance (Mar 11, 2022)
4-1073054-C-T		not specified	Likely benign (Oct 03, 2023)
4-1073147-C-A		not specified	Uncertain significance (Sep 16, 2021)
4-1073152-T-G		not specified	Uncertain significance (Sep 16, 2021)
4-1073620-G-A		not specified	Uncertain significance (Apr 27, 2023)
4-1081581-T-C		not specified	Uncertain significance (Feb 27, 2024)
4-1084399-G-A		Recombination rate quantitative trait locus 1	association (Mar 07, 2008)
4-1085911-A-G		not specified	Uncertain significance (Dec 01, 2022)
4-1085944-A-G		Breast ductal adenocarcinoma	Uncertain significance (Jul 20, 2015)
4-1093477-T-C			Benign (Apr 19, 2019)
4-1093539-GAC-G		Non-obstructive azoospermia	Uncertain significance (Mar 16, 2022)
4-1093699-G-A		not specified	Benign (Mar 28, 2016)
4-1096804-T-C		not specified	Uncertain significance (Jan 26, 2022)
4-1096811-A-G		not specified	Uncertain significance (Apr 10, 2023)
4-1096832-G-A		not specified	Uncertain significance (Mar 17, 2023)
4-1101493-A-G		Recombination rate quantitative trait locus 1	association (Mar 07, 2008)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF212	protein_coding	protein_coding	ENST00000433731	10	57313

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00156	0.972	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0706	162	165	0.985	0.00000834	1927
Missense in Polyphen		36	40.85	0.88127		491
Synonymous	0.167	64	65.7	0.974	0.00000399	559
Loss of Function	1.95	7	15.2	0.460	6.43e-7	193

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000530	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: SUMO E3 ligase that acts as a regulator of crossing-over during meiosis: required to couple chromosome synapsis to the formation of crossover-specific recombination complexes. Localizes to recombination sites and stabilizes meiosis-specific recombination factors, such as MutS-gamma complex proteins (MSH4 and MSH5) and TEX11. May mediate sumoylation of target proteins MSH4 and/or MSH5, leading to enhance their binding to recombination sites. Acts as a limiting factor for crossover designation and/or reinforcement and plays an antagonist role with CCNB1IP1/HEI10 in the regulation of meiotic recombination (By similarity). {ECO:0000250}.

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.259
• ghis: 0.505

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0958

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf212
• Phenotype: reproductive system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: meiotic gene conversion;synapsis;reciprocal meiotic recombination;protein sumoylation;chiasma assembly
• Cellular component: synaptonemal complex
• Molecular function: SUMO transferase activity;metal ion binding