RIPPLY1

ripply transcriptional repressor 1

Basic information

Region (hg38): X:106900062-106903341

Links

ENSG00000147223 ∙ NCBI:92129 ∙ OMIM:300575 ∙ HGNC:25117 ∙ Uniprot:Q0D2K3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cerebellar ataxia, intellectual disability, and dysequilibrium (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RIPPLY1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RIPPLY1 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	2	3
missense			10	2	1	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	3	3

Variants in RIPPLY1

This is a list of pathogenic ClinVar variants found in the RIPPLY1 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-106900765-T-A		not specified	Uncertain significance (Dec 03, 2021)
X-106900793-C-T		not specified	Uncertain significance (Dec 17, 2023)
X-106900812-G-A			Benign (Jun 10, 2018)
X-106900843-T-C		RIPPLY1-related disorder • not specified	Conflicting classifications of pathogenicity (Oct 27, 2022)
X-106900874-G-A		RIPPLY1-related disorder	Likely benign (Mar 21, 2022)
X-106900889-G-A		not specified	Uncertain significance (Aug 04, 2023)
X-106900897-G-A		not specified	Uncertain significance (Sep 19, 2022)
X-106901485-A-T		not specified	Uncertain significance (May 18, 2023)
X-106901501-G-A			Benign (Dec 20, 2017)
X-106901502-C-T		not specified	Uncertain significance (May 30, 2023)
X-106901507-G-T		not specified	Uncertain significance (Dec 27, 2023)
X-106901514-C-T			Uncertain significance (Mar 03, 2020)
X-106901521-C-T			Benign (Dec 20, 2017)
X-106902183-G-T		RIPPLY1-related disorder	Likely benign (Apr 11, 2023)
X-106903178-G-T		not specified	Uncertain significance (Dec 07, 2023)
X-106903194-G-T		not specified	Uncertain significance (Jun 01, 2023)
X-106903280-G-A		not specified	Uncertain significance (Apr 22, 2024)
X-106903281-A-G		not specified	Likely benign (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RIPPLY1	protein_coding	protein_coding	ENST00000276173	4	3273

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00944	0.609	121163	1	3	121167	0.0000165

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.112	49	51.3	0.956	0.00000363	964
Missense in Polyphen		15	15.345	0.97753		299
Synonymous	-0.0436	21	20.7	1.01	0.00000152	305
Loss of Function	0.310	3	3.64	0.824	2.30e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000298	0.000225
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000298	0.000225
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in somitogenesis. Essential for transcriptional repression of the segmental patterning genes, thus terminating the segmentation program in the presomitic mesoderm, and also required for the maintenance of rostrocaudal polarity in somites (By similarity). {ECO:0000250|UniProtKB:Q2WG80}.

Intolerance Scores

• loftool: 0.524
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.28

Haploinsufficiency Scores

• pHI: 0.361
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ripply1
• Phenotype: embryo phenotype; skeleton phenotype

Zebrafish Information Network

• Gene name: ripply1
• Affected structure: slow muscle cell
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;somite specification;embryonic pattern specification;somite rostral/caudal axis specification;negative regulation of transcription, DNA-templated
• Cellular component: nucleus
• Molecular function: protein binding