NEUROG2

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

Basic information

Region (hg38): 4:112513516-112516180

Links

ENSG00000178403 ∙ NCBI:63973 ∙ OMIM:606624 ∙ HGNC:13805 ∙ Uniprot:Q9H2A3 ∙ 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 NEUROG2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEUROG2 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						0
missense			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	0

Variants in NEUROG2

This is a list of pathogenic ClinVar variants found in the NEUROG2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-112514670-C-G		not specified	Uncertain significance (Sep 14, 2022)
4-112514688-G-A		not specified	Uncertain significance (Jul 14, 2022)
4-112514739-G-A		not specified	Uncertain significance (Mar 07, 2025)
4-112514772-C-T		not specified	Uncertain significance (Oct 05, 2023)
4-112514874-A-G		not specified	Uncertain significance (Aug 02, 2023)
4-112514877-G-A		not specified	Uncertain significance (Apr 26, 2023)
4-112514887-C-G		not specified	Uncertain significance (Aug 20, 2024)
4-112514892-C-G		not specified	Uncertain significance (Dec 21, 2022)
4-112514946-C-T		not specified	Uncertain significance (Feb 23, 2023)
4-112514971-G-T		not specified	Uncertain significance (Mar 09, 2025)
4-112514998-A-T		not specified	Uncertain significance (Feb 26, 2025)
4-112515023-G-C		not specified	Uncertain significance (Feb 21, 2025)
4-112515051-A-T		not specified	Uncertain significance (Jun 11, 2021)
4-112515085-C-A		not specified	Uncertain significance (Oct 25, 2024)
4-112515098-G-T		not specified	Uncertain significance (Sep 27, 2021)
4-112515141-G-T		not specified	Uncertain significance (Aug 30, 2021)
4-112515147-T-C		not specified	Uncertain significance (Dec 20, 2024)
4-112515150-A-T		not specified	Uncertain significance (May 27, 2022)
4-112515183-C-T		not specified	Uncertain significance (Feb 07, 2025)
4-112515192-G-A		not specified	Uncertain significance (Apr 18, 2023)
4-112515207-G-A		not specified	Uncertain significance (Mar 31, 2024)
4-112515264-G-A		not specified	Uncertain significance (Nov 27, 2023)
4-112515291-C-T		not specified	Uncertain significance (Sep 11, 2024)
4-112515318-C-G		not specified	Likely benign (Feb 27, 2024)
4-112515322-G-A		not specified	Uncertain significance (Jan 07, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEUROG2	protein_coding	protein_coding	ENST00000313341	1	2657

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.811	0.185	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.427	140	155	0.903	0.00000698	1677
Missense in 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

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: Transcriptional regulator. Involved in neuronal differentiation. Activates transcription by binding to the E box (5'-CANNTG-3').
• Pathway: Dopaminergic Neurogenesis (Consensus)

Recessive Scores

• pRec: 0.250

Intolerance Scores

• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.06

Haploinsufficiency Scores

• pHI: 0.306
• hipred: N
• hipred_score: 0.482
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.979

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Neurog2
• Phenotype: 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;neuron differentiation;positive regulation of DNA-binding transcription factor activity
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;protein dimerization activity;E-box binding