CDR2

cerebellar degeneration related protein 2

Basic information

Region (hg38): 16:22345936-22437165

Links

ENSG00000140743 ∙ NCBI:1039 ∙ OMIM:117340 ∙ HGNC:1799 ∙ Uniprot:Q01850 ∙ 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 CDR2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDR2 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			25	2		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	3	0

Variants in CDR2

This is a list of pathogenic ClinVar variants found in the CDR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-22346987-C-T		not specified	Uncertain significance (Mar 05, 2024)
16-22347011-A-G		not specified	Uncertain significance (Jul 14, 2021)
16-22347038-C-G		not specified	Uncertain significance (Dec 15, 2023)
16-22347071-G-A		not specified	Uncertain significance (Jun 12, 2023)
16-22347086-G-A		not specified	Uncertain significance (Dec 05, 2022)
16-22347093-C-A		not specified	Uncertain significance (Jan 10, 2023)
16-22347093-C-T		not specified	Uncertain significance (Apr 07, 2022)
16-22347126-C-A		not specified	Uncertain significance (Sep 20, 2023)
16-22347146-T-C		not specified	Uncertain significance (Jul 25, 2023)
16-22347246-C-T		not specified	Uncertain significance (Mar 19, 2024)
16-22347267-C-T		not specified	Uncertain significance (Dec 08, 2021)
16-22347354-C-T		not specified	Uncertain significance (Mar 01, 2023)
16-22347397-A-T		not specified	Uncertain significance (Apr 04, 2023)
16-22347407-C-A		not specified	Uncertain significance (Jan 23, 2024)
16-22347408-G-A		not specified	Uncertain significance (Aug 30, 2021)
16-22347599-C-T		not specified	Uncertain significance (Nov 17, 2022)
16-22347654-C-G		not specified	Uncertain significance (Feb 27, 2023)
16-22347683-C-T		not specified	Uncertain significance (Jan 23, 2023)
16-22349322-C-T		not specified	Uncertain significance (Mar 28, 2024)
16-22349325-G-A		not specified	Likely benign (Nov 06, 2023)
16-22349340-A-T		not specified	Uncertain significance (Apr 13, 2023)
16-22349348-G-A		not specified	Uncertain significance (Jan 08, 2024)
16-22349400-G-A		not specified	Uncertain significance (Jun 16, 2023)
16-22349411-T-C		not specified	Uncertain significance (Jan 09, 2024)
16-22349746-T-C		not specified	Uncertain significance (Feb 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDR2	protein_coding	protein_coding	ENST00000268383	5	91230

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.30e-7	0.837	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.853	210	248	0.848	0.0000142	2978
Missense in Polyphen		69	81.744	0.8441		1050
Synonymous	-1.52	124	104	1.19	0.00000645	860
Loss of Function	1.48	13	20.2	0.645	0.00000104	240

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000206
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000185	0.000185
Middle Eastern	0.00	0.00
South Asian	0.000163	0.000163
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.225

Intolerance Scores

• loftool: 0.656
• rvis_EVS: -0.98
• rvis_percentile_EVS: 8.75

Haploinsufficiency Scores

• pHI: 0.228
• hipred: N
• hipred_score: 0.257
• ghis: 0.607

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.250

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdr2
• Phenotype: normal phenotype

Gene ontology

• Cellular component: cytoplasm
• Molecular function: molecular_function;protein binding