CWF19L1

CWF19 like cell cycle control factor 1, the group of Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 10:100232298-100267680

Links

ENSG00000095485 ∙ NCBI:55280 ∙ OMIM:616120 ∙ HGNC:25613 ∙ Uniprot:Q69YN2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive spinocerebellar ataxia 17 (Moderate), mode of inheritance: AR
• autosomal recessive spinocerebellar ataxia 17 (Supportive), mode of inheritance: AR
• autosomal recessive spinocerebellar ataxia 17 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spinocerebellar ataxia, autosomal recessive 17	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	15981765; 25361784

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CWF19L1 gene.

• Autosomal recessive spinocerebellar ataxia 17 (6 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CWF19L1 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				8	3	11
missense		4	40	4	5	53
nonsense	4	2	1			7
start loss						0
frameshift	2	4				6
inframe indel			1			1
splice donor/acceptor (+/-2bp)	3	4				7
splice region			1	3	1	5
non coding						0
Total	9	14	42	12	8

Highest pathogenic variant AF is 0.0000657

Variants in CWF19L1

This is a list of pathogenic ClinVar variants found in the CWF19L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-100233267-C-T			Benign (Dec 31, 2019)
10-100233273-C-T		Inborn genetic diseases	Uncertain significance (Dec 13, 2021)
10-100233276-C-T		Autosomal recessive spinocerebellar ataxia 17 • CWF19L1-related disorder	Benign (May 04, 2023)
10-100233286-TCTC-T		Autosomal recessive spinocerebellar ataxia 17	Uncertain significance (Oct 29, 2021)
10-100233292-C-T		Autosomal recessive spinocerebellar ataxia 17	Likely pathogenic (Jun 01, 2022)
10-100233301-T-C			Uncertain significance (Jul 01, 2023)
10-100233321-C-T		Autosomal recessive spinocerebellar ataxia 17	Uncertain significance (Apr 22, 2022)
10-100233333-T-A			Benign (Dec 31, 2019)
10-100235671-CAA-C		Inborn genetic diseases	Conflicting classifications of pathogenicity (Oct 17, 2022)
10-100235720-T-G		CWF19L1-related disorder	Likely benign (Oct 01, 2023)
10-100235744-T-G			Benign (Jul 04, 2018)
10-100235745-G-A		Autosomal recessive spinocerebellar ataxia 17	Uncertain significance (Oct 16, 2022)
10-100235749-C-T		Inborn genetic diseases	Uncertain significance (Nov 21, 2022)
10-100235758-G-A			Likely pathogenic (Apr 01, 2023)
10-100235766-T-C		Autosomal recessive spinocerebellar ataxia 17	Pathogenic (Mar 23, 2023)
10-100236842-T-C			Benign (Dec 31, 2019)
10-100236843-G-T			Likely benign (May 08, 2018)
10-100236880-C-A		Inborn genetic diseases	Uncertain significance (May 14, 2024)
10-100236941-G-A		Inborn genetic diseases	Uncertain significance (Feb 14, 2023)
10-100236957-G-C		Inborn genetic diseases	Uncertain significance (Apr 06, 2022)
10-100236962-G-A		Inborn genetic diseases	Uncertain significance (May 24, 2023)
10-100236976-G-T			Benign/Likely benign (Feb 01, 2024)
10-100238117-T-TC		Autosomal recessive spinocerebellar ataxia 17	Likely pathogenic (Dec 03, 2018)
10-100238124-C-T		CWF19L1-related disorder	Likely benign (Jun 14, 2019)
10-100238126-C-A		Autosomal recessive spinocerebellar ataxia 17	Likely pathogenic (Jun 19, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CWF19L1	protein_coding	protein_coding	ENST00000354105	14	35383

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.44e-15	0.0866	125610	0	137	125747	0.000545

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	232	284	0.817	0.0000140	3529
Missense in Polyphen		64	79.96	0.8004		961
Synonymous	1.01	88	101	0.872	0.00000490	998
Loss of Function	0.887	26	31.4	0.829	0.00000156	382

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00116	0.00116
Ashkenazi Jewish	0.00	0.00
East Asian	0.00142	0.00141
Finnish	0.00143	0.00143
European (Non-Finnish)	0.000432	0.000431
Middle Eastern	0.00142	0.00141
South Asian	0.000131	0.000131
Other	0.000330	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0825

Intolerance Scores

• loftool: 0.901
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.69

Haploinsufficiency Scores

• pHI: 0.173
• hipred: N
• hipred_score: 0.196
• ghis: 0.483

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00112

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cwf19l1

Zebrafish Information Network

• Gene name: cwf19l1
• Affected structure: cerebellum
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function