RAVER1

ribonucleoprotein, PTB binding 1, the group of RNA binding motif containing

Basic information

Region (hg38): 19:10316212-10333529

Links

ENSG00000161847 ∙ NCBI:125950 ∙ OMIM:609950 ∙ HGNC:30296 ∙ Uniprot:Q8IY67 ∙ 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 RAVER1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAVER1 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					1	1
missense			43			43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	0	1

Variants in RAVER1

This is a list of pathogenic ClinVar variants found in the RAVER1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-10317458-A-G		not specified	Uncertain significance (Dec 07, 2024)
19-10317501-C-T		not specified	Uncertain significance (Nov 11, 2024)
19-10317549-C-T		not specified	Uncertain significance (Nov 11, 2024)
19-10317588-C-T		not specified	Uncertain significance (Nov 25, 2024)
19-10317730-C-T		not specified	Uncertain significance (Jun 21, 2023)
19-10317746-C-T		not specified	Uncertain significance (Jan 31, 2023)
19-10318333-C-T		not specified	Uncertain significance (Jul 02, 2024)
19-10318342-G-A		not specified	Uncertain significance (Oct 04, 2024)
19-10318355-A-T		not specified	Uncertain significance (Jan 03, 2022)
19-10318363-G-A		not specified	Uncertain significance (Jun 25, 2024)
19-10318372-T-C		not specified	Uncertain significance (Dec 04, 2024)
19-10319170-T-C		not specified	Uncertain significance (Apr 22, 2022)
19-10319173-C-A		not specified	Uncertain significance (Mar 14, 2023)
19-10319173-C-T		not specified	Uncertain significance (Feb 12, 2024)
19-10319206-C-T		not specified	Uncertain significance (Apr 25, 2023)
19-10319228-G-A		not specified	Uncertain significance (Mar 11, 2024)
19-10320666-C-T		not specified	Uncertain significance (Sep 12, 2023)
19-10320707-C-T		not specified	Uncertain significance (Dec 27, 2023)
19-10320735-G-A		not specified	Uncertain significance (Oct 20, 2024)
19-10320831-C-T		Inborn genetic diseases	Uncertain significance (Nov 23, 2021)
19-10320845-C-T		not specified	Uncertain significance (Nov 26, 2024)
19-10321106-C-T		not specified	Uncertain significance (Jan 16, 2024)
19-10321123-G-T			Benign (Aug 23, 2018)
19-10321127-G-T		not specified	Uncertain significance (Aug 08, 2022)
19-10321190-C-A		not specified	Uncertain significance (Oct 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAVER1	protein_coding	protein_coding	ENST00000293677	13	17429

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.911	0.0890	124545	0	14	124559	0.0000562

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.46	324	407	0.797	0.0000262	4678
Missense in Polyphen		130	189.13	0.68735		1958
Synonymous	0.241	189	193	0.978	0.0000128	1699
Loss of Function	3.94	4	25.4	0.157	0.00000130	319

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000305	0.000287
Ashkenazi Jewish	0.000102	0.0000995
East Asian	0.0000561	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000571	0.0000532
Middle Eastern	0.0000561	0.0000556
South Asian	0.00	0.00
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cooperates with PTBP1 to modulate regulated alternative splicing events. Promotes exon skipping. Cooperates with PTBP1 to modulate switching between mutually exclusive exons during maturation of the TPM1 pre-mRNA (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.54

Haploinsufficiency Scores

• pHI: 0.216
• hipred: Y
• hipred_score: 0.701
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.944

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Raver1
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Cellular component: nucleus;cytoplasm
• Molecular function: RNA binding