DNER

delta/notch like EGF repeat containing

Basic information

Region (hg38): 2:229357628-229714555

Links

ENSG00000187957 ∙ NCBI:92737 ∙ OMIM:607299 ∙ HGNC:24456 ∙ Uniprot:Q8NFT8 ∙ 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 DNER gene.

Variants pathogenicity by type

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

Variants in DNER

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

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

Position	Type	Phenotype	Significance	ClinVar
2-229358629-C-T		not specified	Uncertain significance (Mar 06, 2023)
2-229366881-C-T			Benign (Jul 26, 2018)
2-229366882-C-T		not specified	Uncertain significance (Jun 18, 2021)
2-229367030-C-T		not specified	Uncertain significance (Feb 06, 2023)
2-229367084-G-A		not specified	Uncertain significance (Jan 23, 2024)
2-229367096-T-C			Likely benign (Jul 26, 2018)
2-229367103-G-A			Benign (Jul 31, 2018)
2-229367112-T-C			Benign (May 03, 2018)
2-229388294-T-C		not specified	Uncertain significance (Apr 20, 2024)
2-229407256-A-G		not specified	Uncertain significance (Nov 30, 2021)
2-229407275-G-A			Benign (Apr 12, 2018)
2-229418143-T-C		not specified	Uncertain significance (Apr 06, 2023)
2-229447328-G-A		not specified	Uncertain significance (Dec 17, 2021)
2-229447354-C-T		not specified	Uncertain significance (Oct 26, 2022)
2-229447359-C-T			Likely benign (Sep 01, 2022)
2-229447370-C-A		not specified	Uncertain significance (Aug 21, 2023)
2-229447457-C-T		not specified	Uncertain significance (Jun 27, 2022)
2-229447500-G-A			Benign (Jul 26, 2018)
2-229447508-C-T		not specified	Uncertain significance (Dec 12, 2023)
2-229477170-G-C		not specified	Uncertain significance (Mar 21, 2023)
2-229477221-C-T		not specified	Uncertain significance (Feb 02, 2024)
2-229477226-T-C		not specified	Uncertain significance (Mar 27, 2023)
2-229512819-G-T		not specified	Uncertain significance (May 08, 2024)
2-229512842-C-T		not specified	Uncertain significance (Dec 21, 2023)
2-229512845-G-A		not specified	Uncertain significance (Oct 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DNER	protein_coding	protein_coding	ENST00000341772	13	356930

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.186	0.814	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.565	366	398	0.920	0.0000225	4800
Missense in Polyphen		82	123.05	0.6664		1384
Synonymous	-1.92	188	157	1.19	0.0000102	1429
Loss of Function	4.02	8	32.9	0.243	0.00000167	395

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000493	0.000490
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000169	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000446	0.0000439
Middle Eastern	0.000169	0.000163
South Asian	0.000198	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Activator of the NOTCH1 pathway. May mediate neuron-glia interaction during astrocytogenesis (By similarity). {ECO:0000250}.
• Pathway: Vitamin D Receptor Pathway;Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Canonical and Non-canonical Notch signaling;Signal Transduction;Signaling by NOTCH1;Signaling by NOTCH;Notch signaling pathway;Activated NOTCH1 Transmits Signal to the Nucleus (Consensus)

Recessive Scores

• pRec: 0.240

Intolerance Scores

• loftool: 0.0647
• rvis_EVS: -1.02
• rvis_percentile_EVS: 8.1

Haploinsufficiency Scores

• pHI: 0.263
• hipred: Y
• hipred_score: 0.783
• ghis: 0.567

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.447

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dner
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: dner
• Affected structure: neural precursor cell proliferation
• Phenotype tag: abnormal
• Phenotype quality: increased rate

Gene ontology

• Biological process: neuron migration;endocytosis;Notch signaling pathway;Notch receptor processing;synapse assembly;central nervous system development;glial cell differentiation;skeletal muscle fiber development
• Cellular component: early endosome;plasma membrane;integral component of membrane;dendrite;neuronal cell body
• Molecular function: transmembrane signaling receptor activity;Notch binding;calcium ion binding;protein binding;clathrin binding