R3HCC1

R3H domain and coiled-coil containing 1

Basic information

Region (hg38): 8:23270120-23296279

Links

ENSG00000104679 ∙ NCBI:203069 ∙ ∙ HGNC:27329 ∙ Uniprot:Q9Y3T6 ∙ 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 R3HCC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the R3HCC1 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			16	3		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	3	0

Variants in R3HCC1

This is a list of pathogenic ClinVar variants found in the R3HCC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-23290315-G-A		not specified	Likely benign (Oct 25, 2023)
8-23290375-G-C		not specified	Uncertain significance (Nov 29, 2023)
8-23290401-G-A		not specified	Uncertain significance (Apr 30, 2024)
8-23290459-T-C		not specified	Uncertain significance (Mar 25, 2022)
8-23291391-C-G		not specified	Uncertain significance (May 23, 2024)
8-23291407-A-G		not specified	Uncertain significance (Sep 01, 2021)
8-23291500-C-A		not specified	Uncertain significance (Jul 20, 2022)
8-23291517-A-G		not specified	Likely benign (Jan 30, 2024)
8-23293362-G-T		not specified	Uncertain significance (Jan 29, 2024)
8-23294786-C-T		not specified	Uncertain significance (Oct 29, 2021)
8-23294794-C-A		not specified	Uncertain significance (Dec 21, 2022)
8-23294796-C-T		not specified	Uncertain significance (Jul 19, 2023)
8-23294810-C-T		not specified	Uncertain significance (Dec 21, 2023)
8-23295975-C-T		not specified	Uncertain significance (Apr 19, 2024)
8-23295976-G-A		not specified	Uncertain significance (Aug 11, 2022)
8-23296018-G-A		not specified	Uncertain significance (Apr 25, 2023)
8-23296026-G-A		not specified	Uncertain significance (May 28, 2024)
8-23296032-C-T		not specified	Uncertain significance (Dec 27, 2023)
8-23296056-A-G		not specified	Uncertain significance (Jan 26, 2022)
8-23296069-C-G		not specified	Uncertain significance (Jan 23, 2024)
8-23296077-C-T		not specified	Uncertain significance (Mar 23, 2023)
8-23296078-G-A		not specified	Likely benign (Jul 25, 2023)
8-23296090-C-T		not specified	Uncertain significance (Mar 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
R3HCC1	protein_coding	protein_coding	ENST00000265806	5	26160

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000143	0.670	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.775	118	144	0.818	0.00000867	1611
Missense in Polyphen		34	38.11	0.89216		412
Synonymous	-0.286	66	63.1	1.05	0.00000393	515
Loss of Function	0.835	7	9.82	0.713	4.12e-7	135

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

Intolerance Scores

• rvis_EVS: 0.3
• rvis_percentile_EVS: 72.01

Haploinsufficiency Scores

• pHI: 0.142
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.384

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: R3hcc1

Gene ontology

• Cellular component: exon-exon junction complex
• Molecular function: nucleic acid binding