NEUROG2

protein-coding

neurogenin 2, the group of Basic helix-loop-helix proteins

Gene summary

This gene encodes a neural-specific basic helix-loop-helix (bHLH) transcription factor that can specify a neuronal fate on ectodermal cells and is expressed in neural progenitor cells within the developing central and peripheral nervous systems. The protein product of this gene also plays a role in the differentiation and survival of midbrain dopaminergic neurons. [provided by RefSeq, Apr 2012]

MANE transcript

NM_024019.4

Inheritance

—

ClinVar variants

U:44B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr4:112,513,516-112,516,180

External References & Databases

Ensembl (ENSG00000178403)

Transcript & Mutation Effects

hg38 • Region Span ~2.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NEUROG2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 47

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024019.4. 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				1 clinvar		1
missense			44 clinvar	2 clinvar		46
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	44	3	0	47

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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_024019.4	RefSeq	NP_076924.1	1	MANE Select
ENST00000313341.4	Ensembl	ENSP00000317333.3	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Dopaminergic Neurogenesis

Biological Process

regulation of transcription by RNA polymerase II
neuron differentiation
positive regulation of DNA-binding transcription factor activity

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
protein dimerization activity
E-box binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000313341
Coding exons: 1
Length: 2657
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	0.427	140	155	0.903	0.00000698	1677
Missense (PolyPhen)		40	56.526	0.70764		569
Synonymous	-0.975	85	74.3	1.14	0.00000351	617
Loss of Function	2.17	0	5.50	0.00	2.37e-7	69

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: Transcriptional regulator. Involved in neuronal differentiation. Activates transcription by binding to the E box (5'-CANNTG-3').;

Recessive Scores

pRec: 0.250

Intolerance Scores

RVIS EVS: 0.26
RVIS percentile EVS: 70.06

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.979

Gene Damage Prediction

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