NEUROD4

neuronal differentiation 4, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 12:55019974-55030017

Links

ENSG00000123307 ∙ NCBI:58158 ∙ OMIM:611635 ∙ HGNC:13802 ∙ Uniprot:Q9HD90 ∙ 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 NEUROD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEUROD4 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			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	1

Variants in NEUROD4

This is a list of pathogenic ClinVar variants found in the NEUROD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-55026453-T-C		not specified	Uncertain significance (Oct 03, 2024)
12-55026491-C-T		not specified	Uncertain significance (Feb 01, 2025)
12-55026632-G-C		not specified	Uncertain significance (Nov 10, 2022)
12-55026659-A-G		not specified	Uncertain significance (Dec 20, 2021)
12-55026680-C-T		not specified	Uncertain significance (May 17, 2023)
12-55026721-C-G			Benign (Feb 25, 2018)
12-55026765-A-G		not specified	Uncertain significance (Aug 19, 2024)
12-55026801-A-C		not specified	Uncertain significance (Nov 10, 2024)
12-55026852-C-T		not specified	Uncertain significance (Aug 12, 2024)
12-55026963-A-G		not specified	Uncertain significance (Apr 13, 2022)
12-55026968-G-A		not specified	Uncertain significance (Mar 27, 2023)
12-55026969-G-A		not specified	Uncertain significance (Mar 07, 2025)
12-55026983-C-T		not specified	Uncertain significance (Aug 10, 2021)
12-55027002-A-G		not specified	Uncertain significance (Apr 20, 2024)
12-55027016-T-C		not specified	Uncertain significance (Jan 22, 2025)
12-55027025-G-A		not specified	Likely benign (Oct 12, 2022)
12-55027059-C-T		not specified	Uncertain significance (Jun 01, 2022)
12-55027073-C-T		not specified	Uncertain significance (Jul 31, 2024)
12-55027100-C-T		not specified	Uncertain significance (Nov 30, 2022)
12-55027191-G-A		not specified	Uncertain significance (Aug 19, 2024)
12-55027265-T-A		not specified	Uncertain significance (Nov 09, 2022)
12-55027283-C-T		not specified	Uncertain significance (Feb 22, 2025)
12-55027300-T-G		not specified	Uncertain significance (Jan 08, 2024)
12-55027350-G-A		not specified	Uncertain significance (Jan 03, 2024)
12-55027391-C-T		not specified	Uncertain significance (Dec 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEUROD4	protein_coding	protein_coding	ENST00000242994	1	10070

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0970	0.871	125723	1	19	125743	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.567	200	179	1.12	0.00000875	2173
Missense in Polyphen		75	73.538	1.0199		858
Synonymous	-0.845	77	68.1	1.13	0.00000330	663
Loss of Function	1.84	3	8.91	0.337	5.22e-7	117

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000296	0.000296
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000619	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably acts as a transcriptional activator. Mediates neuronal differentiation. Required for the regulation of amacrine cell fate specification in the retina (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.243
• rvis_EVS: 0.88
• rvis_percentile_EVS: 89.07

Haploinsufficiency Scores

• pHI: 0.413
• hipred: N
• hipred_score: 0.444
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.820

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Neurod4
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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); vision/eye phenotype; growth/size/body region phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: neurod4
• Affected structure: olfactory placode
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: neuron migration;regulation of transcription by RNA polymerase II;Notch signaling pathway;neuroblast proliferation;glial cell differentiation;amacrine cell differentiation;cell fate commitment;positive regulation of cell differentiation;neuron development
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein dimerization activity