NEUROG1

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

Basic information

Region (hg38): 5:135534281-135535964

Previous symbols: [ "NEUROD3" ]

Links

ENSG00000181965 ∙ NCBI:4762 ∙ OMIM:601726 ∙ HGNC:7764 ∙ Uniprot:Q92886 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cranial dysinnervation disorder, congenital, with absent corneal reflex and developmental delay	AR	Audiologic/Otolaryngologic	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	Audiologic/Otolaryngologic; Craniofacial; Neurologic; Ophthalmologic	23419067; 26077850; 33439489; 36647078

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NEUROG1 gene.

• Inborn genetic diseases (10 variants)
• not provided (3 variants)
• Cranial dysinnervation disorder, congenital, with absent corneal reflex and developmental delay (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEUROG1 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			10		2	12
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	10	0	3

Variants in NEUROG1

This is a list of pathogenic ClinVar variants found in the NEUROG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-135534996-C-T		not specified	Uncertain significance (Jan 26, 2023)
5-135535143-G-A		not specified	Uncertain significance (Mar 31, 2023)
5-135535143-G-C		not specified	Uncertain significance (Jun 09, 2022)
5-135535143-G-T			Benign (Mar 29, 2018)
5-135535168-C-G		not specified	Uncertain significance (May 03, 2023)
5-135535207-C-T		not specified	Uncertain significance (Oct 20, 2023)
5-135535210-G-A		not specified	Uncertain significance (Oct 22, 2021)
5-135535344-C-A		Cranial dysinnervation disorder, congenital, with absent corneal reflex and developmental delay	Pathogenic (Aug 16, 2023)
5-135535459-T-TCCGG		See cases • Cranial dysinnervation disorder, congenital, with absent corneal reflex and developmental delay	Likely pathogenic (Feb 17, 2021)
5-135535483-C-T		not specified	Uncertain significance (Dec 16, 2021)
5-135535489-C-A		Cranial dysinnervation disorder, congenital, with absent corneal reflex and developmental delay	Pathogenic (Aug 16, 2023)
5-135535503-C-A		not specified	Uncertain significance (Mar 02, 2023)
5-135535503-C-T		not specified	Uncertain significance (May 23, 2023)
5-135535550-C-T			Benign (Mar 29, 2018)
5-135535560-G-A		not specified	Uncertain significance (May 17, 2023)
5-135535576-C-T		not specified	Uncertain significance (Nov 12, 2021)
5-135535590-C-T			Benign (Dec 31, 2019)
5-135535642-T-C		not specified	Uncertain significance (Dec 09, 2023)
5-135535647-G-A		not specified	Uncertain significance (Mar 04, 2024)
5-135535648-C-A		not specified	Uncertain significance (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEUROG1	protein_coding	protein_coding	ENST00000314744	1	1649

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000217	0.312	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.801	164	138	1.19	0.00000634	1489
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Neural Crest Differentiation;Regulation of nuclear beta catenin signaling and target gene transcription (Consensus)

Recessive Scores

• pRec: 0.386

Intolerance Scores

• loftool: 0.308
• rvis_EVS: 0.5
• rvis_percentile_EVS: 79.89

Haploinsufficiency Scores

• pHI: 0.648
• hipred: N
• hipred_score: 0.367

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.999

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Neurog1
• Phenotype: cellular 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); 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)

Zebrafish Information Network

• Gene name: neurog1
• Affected structure: neuromast hair cell
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;thorax and anterior abdomen determination;nervous system development;trigeminal nerve development;vestibulocochlear nerve formation;neuron differentiation;peristalsis;auditory behavior;positive regulation of exit from mitosis;genitalia morphogenesis;inner ear morphogenesis;cell fate commitment;positive regulation of neuron differentiation;positive regulation of transcription by RNA polymerase II;regulation of muscle organ development;genitalia development;inner ear development;neuromuscular process controlling balance;positive regulation of DNA-binding transcription factor activity;mastication;cochlea development;cochlea morphogenesis;craniofacial suture morphogenesis;learned vocalization behavior;negative regulation of relaxation of muscle;negative regulation of saliva secretion;hard palate morphogenesis
• Cellular component: nucleus;perikaryon
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;chromatin binding;DNA-binding transcription factor activity;protein binding;protein homodimerization activity;E-box binding;sequence-specific double-stranded DNA binding