CDNF

cerebral dopamine neurotrophic factor

Basic information

Region (hg38): 10:14819244-14838575

Previous symbols: [ "ARMETL1" ]

Links

ENSG00000185267 ∙ NCBI:441549 ∙ OMIM:611233 ∙ HGNC:24913 ∙ Uniprot:Q49AH0 ∙ 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 CDNF gene.

• not provided (2 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

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

Variants in CDNF

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

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

Position	Type	Phenotype	Significance	ClinVar
10-14820043-A-G			Benign (Dec 31, 2019)
10-14820141-C-A			Benign (Dec 31, 2019)
10-14825501-G-T		not specified	Uncertain significance (Nov 05, 2021)
10-14838451-G-C		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDNF	protein_coding	protein_coding	ENST00000465530	4	19326

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.13e-7	0.148	125682	0	66	125748	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.290	94	102	0.919	0.00000516	1207
Missense in Polyphen		29	31.927	0.90832		411
Synonymous	1.28	29	39.2	0.739	0.00000197	353
Loss of Function	-0.291	9	8.11	1.11	4.25e-7	102

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00103	0.00101
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000281	0.000281
Middle Eastern	0.0000544	0.0000544
South Asian	0.000107	0.0000980
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Trophic factor for dopamine neurons. Prevents the 6- hydroxydopamine (6-OHDA)-induced degeneration of dopaminergic neurons. When administered after 6-OHDA-lesioning, restores the dopaminergic function and prevents the degeneration of dopaminergic neurons in substantia nigra (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.508
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.49

Haploinsufficiency Scores

• pHI: 0.117
• hipred: N
• hipred_score: 0.282
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.367

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdnf

Gene ontology

• Biological process: regulation of signaling receptor activity;neuron projection development;dopaminergic neuron differentiation
• Cellular component: extracellular space;endoplasmic reticulum
• Molecular function: growth factor activity