NEUROG1

Chr 5AR

neurogenin 1

Also known as: AKA, CCDDRD, Math4C, NEUROD3, bHLHa6, ngn1

NCBI Gene: 4762ENSG00000181965UniProt: Q92886

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]

Primary Disease Associations & Inheritance

Cranial dysinnervation disorder, congenital, with absent corneal reflex and developmental delayMIM #620469
AR
83
ClinVar variants
17
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— NEUROG1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
17 Pathogenic / Likely Pathogenic· 60 VUS of 83 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.89LOEUF
pLI 0.000
Z-score -0.38
OE 1.20 (0.60–1.89)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.80Z-score
OE missense 1.19 (1.05–1.36)
164 obs / 137.6 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.1.20 (0.60–1.89)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.19 (1.05–1.36)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.26
0≤1.21.6
LoF obs/exp: 5 / 4.2Missense obs/exp: 164 / 137.6Syn Z: -1.60

ClinVar Variant Classifications

83 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic14
Likely Pathogenic3
VUS60
Likely Benign4
Benign2
14
Pathogenic
3
Likely Pathogenic
60
VUS
4
Likely Benign
2
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
1
13
0
14
Likely Pathogenic
1
1
1
0
3
VUS
0
56
4
0
60
Likely Benign
0
1
1
2
4
Benign
0
2
0
0
2
Total16119283

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

NEUROG1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
NEUROGENIN 1; NEUROG1
MIM #601726 · *

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

MIM #620469

Molecular basis of disorder known

Autosomal recessive
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
A novel case of two siblings harbouring homozygous variant in the NEUROG1 gene with autism as an additional phenotype: a case report.
Sheth F et al.·BMC Neurol
2023Review
Basic helix-loop-helix transcription factor NEUROG1 and schizophrenia: effects on illness susceptibility, MRI brain morphometry and cognitive abilities.
Ho BC et al.·Schizophr Res
2008
Adding evidence to the role of NEUROG1 in congenital cranial dysinnervation disorders.
Dupont J et al.·Clin Genet
2021Case report
From Genetics to Histomolecular Characterization: An Insight into Colorectal Carcinogenesis in Lynch Syndrome.
Lepore Signorile M et al.·Int J Mol Sci
2021Review
Hypermethylated DNA as a biomarker for colorectal cancer: a systematic review.
Rasmussen SL et al.·Colorectal Dis
2016Review
Diagnostic power of DNA methylation markers suggestive of cholangiocarcinoma in ERCP-based brush cytology.
Prachayakul V et al.·Gastrointest Endosc
2022
Neurologic and ocular phenotype in Pitt-Hopkins syndrome and a zebrafish model.
Brockschmidt A et al.·Hum Genet
2011Case report
Exploring the Functional Heterogeneity of Directly Reprogrammed Neural Stem Cell-Derived Neurons via Single-Cell RNA Sequencing.
Kim YS et al.·Cells
2023Functional
A boy with homozygous microdeletion of NEUROG1 presents with a congenital cranial dysinnervation disorder [Moebius syndrome variant].
Schröder JC et al.·Behav Brain Funct
2013
CpG island methylator phenotype, microsatellite instability, BRAF mutation and clinical outcome in colon cancer.
Ogino S et al.·Gut
2009
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Expression dynamics of functionally equivalent Neurog1/2 genes enable protracted neurogenesis and temporal emergence of somatosensory neuron lineages.
Desiderio S et al.·Cell Rep
2026Functional
Evaluation of NEUROG1 methylation status in stool specimens in the advanced adenomas and colorectal cancer.
Zhang L et al.·PeerJ
2025🔓 Open Access
Foxp and Skor family proteins control differentiation of Purkinje cells from Ptf1a- and Neurog1-expressing progenitors in zebrafish.
Itoh T et al.·Development
2024🔓 Open AccessFunctional
Neurog1 and Olig2 integrate patterning and neurogenesis signals in development of zebrafish dopaminergic and glutamatergic dual transmitter neurons.
Altbürger C et al.·Dev Biol
2024Functional
Neurog1-Derived Peptides RMNE1 and DualPep-Shine Penetrate the Skin and Inhibit Melanin Synthesis by Regulating MITF Transcription.
Song EC et al.·Int J Mol Sci
2023🔓 Open Access
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools