R3HCC1L

R3H domain and coiled-coil containing 1 like

Basic information

Region (hg38): 10:98134623-98244897

Previous symbols: [ "C10orf28" ]

Links

ENSG00000166024 ∙ NCBI:27291 ∙ ∙ HGNC:23512 ∙ Uniprot:Q7Z5L2 ∙ 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 R3HCC1L gene.

• Inborn genetic diseases (51 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the R3HCC1L 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			47	4		51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	47	5	0

Variants in R3HCC1L

This is a list of pathogenic ClinVar variants found in the R3HCC1L region.

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

Position	Type	Phenotype	Significance	ClinVar
10-98208119-A-C		not specified	Uncertain significance (Sep 12, 2023)
10-98208163-A-G		not specified	Uncertain significance (Jan 29, 2024)
10-98208188-G-A		not specified	Uncertain significance (Apr 22, 2022)
10-98208270-A-C		not specified	Uncertain significance (Dec 19, 2023)
10-98208280-C-G		not specified	Uncertain significance (Aug 12, 2021)
10-98208281-T-C		not specified	Uncertain significance (Jan 08, 2024)
10-98208338-C-G		not specified	Uncertain significance (Oct 05, 2023)
10-98208395-T-C		not specified	Uncertain significance (Dec 14, 2021)
10-98208425-T-A		not specified	Uncertain significance (Dec 26, 2023)
10-98208440-G-T		not specified	Uncertain significance (Dec 19, 2022)
10-98208505-A-G		not specified	Uncertain significance (Oct 12, 2022)
10-98208572-C-T		not specified	Uncertain significance (Jan 31, 2023)
10-98208581-C-T		not specified	Uncertain significance (Sep 12, 2023)
10-98208593-G-T		not specified	Uncertain significance (Oct 12, 2021)
10-98208684-G-T		not specified	Uncertain significance (Oct 13, 2023)
10-98208685-C-T		not specified	Uncertain significance (Mar 07, 2024)
10-98208703-G-A		not specified	Likely benign (Jun 28, 2023)
10-98208713-A-G		not specified	Uncertain significance (Aug 16, 2021)
10-98208740-C-G		not specified	Uncertain significance (May 03, 2023)
10-98208821-C-G		not specified	Uncertain significance (May 10, 2022)
10-98208893-G-A		not specified	Uncertain significance (Dec 20, 2023)
10-98208913-A-T		not specified	Uncertain significance (Oct 12, 2021)
10-98208922-C-A		not specified	Uncertain significance (Jan 03, 2022)
10-98208928-A-G		not specified	Uncertain significance (Oct 25, 2023)
10-98208974-A-G		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
R3HCC1L	protein_coding	protein_coding	ENST00000298999	6	110268

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.26e-9	0.791	125649	0	82	125731	0.000326

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.736	453	411	1.10	0.0000205	5154
Missense in Polyphen		96	102.33	0.93812		1269
Synonymous	-1.49	167	144	1.16	0.00000743	1480
Loss of Function	1.57	18	26.8	0.673	0.00000146	362

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000627	0.000624
Middle Eastern	0.00	0.00
South Asian	0.0000994	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Pathway: TCR (Consensus)

Recessive Scores

• pRec: 0.0701

Intolerance Scores

• rvis_EVS: 3.29
• rvis_percentile_EVS: 99.41

Haploinsufficiency Scores

• pHI: 0.0816
• hipred: N
• hipred_score: 0.173
• ghis: 0.400

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: R3hcc1l
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Cellular component: exon-exon junction complex
• Molecular function: protein binding