NEUROD6

neuronal differentiation 6, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 7:31337464-31340726

Links

ENSG00000164600

∙ NCBI:63974 ∙ OMIM:611513 ∙ HGNC:13804 ∙ Uniprot:Q96NK8 ∙ 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 NEUROD6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEUROD6 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			12 clinvar			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in NEUROD6

This is a list of pathogenic ClinVar variants found in the NEUROD6 region.

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

Position	Phenotype	Significance	ClinVar
7-31338292-G-T	not specified	Uncertain significance (Dec 16, 2023)	3195455
7-31338320-C-T	not specified	Uncertain significance (Nov 18, 2022)	2328160
7-31338338-C-T	not specified	Uncertain significance (Jan 22, 2024)	3195448
7-31338354-C-G	not specified	Uncertain significance (Jul 20, 2021)	2238451
7-31338359-C-A	not specified	Uncertain significance (Mar 30, 2024)	3299386
7-31338362-C-T	not specified	Uncertain significance (Mar 30, 2024)	3299385
7-31338377-C-T	not specified	Uncertain significance (Dec 18, 2023)	3195442
7-31338436-G-C	not specified	Uncertain significance (Mar 30, 2024)	3299384
7-31338595-A-G	not specified	Uncertain significance (Mar 29, 2023)	2530970
7-31338643-G-T	not specified	Uncertain significance (Dec 14, 2022)	2219208
7-31338709-C-T	not specified	Uncertain significance (Aug 28, 2023)	2592839
7-31338785-C-T	not specified	Uncertain significance (Jan 10, 2023)	2454444
7-31339018-G-A	not specified	Uncertain significance (Aug 23, 2021)	2229044
7-31339073-C-G	not specified	Uncertain significance (Feb 12, 2024)	3195420
7-31339090-T-G	not specified	Uncertain significance (Jul 14, 2023)	2612184

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEUROD6	protein_coding	protein_coding	ENST00000297142	1	3434

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.885	0.115	125480	0	2	125482	0.00000797

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.84	112	182	0.615	0.00000997	2232
Missense in Polyphen		22	53.19	0.41361		587
Synonymous	-1.12	86	73.7	1.17	0.00000474	639
Loss of Function	2.86	1	11.4	0.0876	7.41e-7	140

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)	0.0000178	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Activates E box-dependent transcription in collaboration with TCF3/E47. May be a trans-acting factor involved in the development and maintenance of the mammalian nervous system. Transactivates the promoter of its own gene (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.186

Intolerance Scores

loftool: 0.0633
rvis_EVS: -0.27
rvis_percentile_EVS: 33.97

Haploinsufficiency Scores

pHI: 0.721
hipred: Y
hipred_score: 0.809
ghis: 0.610

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Neurod6
Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular 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); normal phenotype; 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);

Gene ontology

Biological process: dentate gyrus development;cell differentiation;positive regulation of transcription by RNA polymerase II
Cellular component: nucleus
Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;protein dimerization activity