NEUROG1

protein-coding

neurogenin 1, the group of Basic helix-loop-helix proteins

Gene summary

Enables E-box binding activity and protein homodimerization activity. Involved in several processes, including cochlea morphogenesis; cranial nerve development; and hard palate morphogenesis. Predicted to be located in chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

NEUROD3

MANE transcript

NM_006161.3

Inheritance

ClinVar variants

P:4U:56B:6

Top phenotype

Cranial dysinnervation disorder, congenital, with absent corneal reflex and developmental delay

gnomAD constraint

pLI —, LoF o/e 1.2

Max pathogenic AF

—

Genomic locus

chr5:135,534,282-135,535,964

External References & Databases

Ensembl (ENSG00000181965)

Transcript & Mutation Effects

hg38 • Region Span ~1.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

cranial dysinnervation disorder, congenital, with absent corneal reflex and developmental delaySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0957563

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Cranial dysinnervation disorder, congenital, with absent corneal reflex and developmental delayAR

Manifestation: Audiologic/Otolaryngologic; Craniofacial; Neurologic; Ophthalmologic

Intervention: Audiologic/Otolaryngologic

Rationale: Among other findings, the condition can include sensorineural hearing loss, and early recognition and treatment of hearing impairment may improve outcomes, including speech and language development

Refs: 23419067; 26077850; 33439489; 36647078

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NEUROG1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 57

not providedTotal: 5

Cranial dysinnervation disorder, congenital, with absent corneal reflex and developmental delayTotal: 5

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006161.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar		3
missense	1 clinvar	1 clinvar	56 clinvar	1 clinvar	2 clinvar	61
nonsense	1 clinvar					1
start loss						0
frameshift		1 clinvar				1
splice donor/acceptor (+/-2bp)						0
Total	2	2	56	4	2	66

Highest pathogenic variant AF is 0.0000038153958

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006161.3	RefSeq	NP_006152.2	1	MANE Select
ENST00000314744.6	Ensembl	ENSP00000317580.4	1	MANE Select

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
neurog1	Danio rerio	Structure: neuromast hair cell Quality: mislocalised abnormal

Gene / Model

Organism

Observed Phenotype

neurog1

Danio rerio

Structure: neuromast hair cell

Quality: mislocalised

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human)
Neural Crest Differentiation
Regulation of nuclear beta catenin signaling and target gene transcription

Biological Process

regulation of transcription by RNA polymerase II
thorax and anterior abdomen determination
nervous system development
trigeminal nerve development
vestibulocochlear nerve formation

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
chromatin binding
DNA-binding transcription factor activity
protein binding
protein homodimerization activity

Cellular Component

nucleus
perikaryon

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000314744
Coding exons: 1
Length: 1649
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.801	164	138	1.19	0.00000634	1489
Missense (PolyPhen)		42	44.43	0.94531		479
Synonymous	-1.60	79	62.9	1.26	0.00000302	536
Loss of Function	-0.381	5	4.16	1.20	1.80e-7	44

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as a transcriptional regulator. Involved in the initiation of neuronal differentiation. Activates transcription by binding to the E box (5'-CANNTG-3'). Associates with chromatin to enhancer regulatory elements in genes encoding key transcriptional regulators of neurogenesis (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.386

Intolerance Scores

LoFtool: 0.308
RVIS EVS: 0.5
RVIS percentile EVS: 79.89

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.999

Gene Damage Prediction

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