RIBC1

RIB43A domain with coiled-coils 1

Basic information

Region (hg38): X:53422690-53431120

Links

ENSG00000158423 ∙ NCBI:158787 ∙ ∙ HGNC:26537 ∙ Uniprot:Q8N443 ∙ 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 RIBC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RIBC1 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			17	2		19
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	17	3	0

Variants in RIBC1

This is a list of pathogenic ClinVar variants found in the RIBC1 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-53422829-C-T			Benign (Jul 15, 2018)
X-53422841-A-G			Likely benign (Aug 25, 2018)
X-53426353-G-A		not specified	Uncertain significance (May 27, 2022)
X-53428031-T-A		not specified	Uncertain significance (Mar 24, 2023)
X-53428046-G-A		not specified	Uncertain significance (Sep 14, 2022)
X-53428049-G-A		not specified	Uncertain significance (Oct 27, 2022)
X-53428082-A-C		not specified	Uncertain significance (Dec 19, 2022)
X-53428405-G-A		not specified	Likely benign (May 06, 2022)
X-53428409-G-A		not specified	Uncertain significance (Jun 22, 2023)
X-53429937-A-G		not specified	Uncertain significance (Jun 19, 2024)
X-53430421-G-A		not specified	Uncertain significance (Apr 07, 2023)
X-53430522-A-G		not specified	Likely benign (Mar 14, 2023)
X-53430544-C-T		not specified	Uncertain significance (Apr 09, 2024)
X-53430582-G-A		not specified	Uncertain significance (Jul 12, 2022)
X-53430617-G-C		not specified	Uncertain significance (Jun 22, 2021)
X-53430633-C-G		not specified	Uncertain significance (Jun 02, 2023)
X-53430642-A-G		not specified	Uncertain significance (Oct 27, 2023)
X-53430649-T-G		not specified	Uncertain significance (Jan 03, 2024)
X-53430657-G-C		not specified	Uncertain significance (Nov 08, 2022)
X-53430679-G-A		not specified	Uncertain significance (May 27, 2022)
X-53430700-A-G		not specified	Uncertain significance (Jan 31, 2024)
X-53430800-A-G			Likely benign (Nov 01, 2022)
X-53430940-T-A			Uncertain significance (Jun 13, 2022)
X-53430951-C-G		not specified	Uncertain significance (Dec 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RIBC1	protein_coding	protein_coding	ENST00000375327	6	8421

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.983	0.0170	125726	0	3	125729	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	125	161	0.776	0.0000139	2494
Missense in Polyphen		23	34.581	0.66511		701
Synonymous	1.34	42	54.6	0.769	0.00000413	691
Loss of Function	3.57	1	16.8	0.0595	0.00000145	218

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000365	0.0000365
Ashkenazi Jewish	0.000141	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000127	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0861

Intolerance Scores

• loftool: 0.388
• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.0827
• hipred: N
• hipred_score: 0.314
• ghis: 0.459

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.434

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ribc1

Gene ontology

• Molecular function: protein binding