ASCL2

achaete-scute family bHLH transcription factor 2, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 11:2268498-2270588

Links

ENSG00000183734 ∙ NCBI:430 ∙ OMIM:601886 ∙ HGNC:739 ∙ Uniprot:Q99929 ∙ 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 ASCL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ASCL2 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in ASCL2

This is a list of pathogenic ClinVar variants found in the ASCL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-2269769-G-C		not specified	Uncertain significance (Nov 15, 2021)
11-2269863-T-C		not specified	Uncertain significance (Jun 11, 2024)
11-2269920-G-A		not specified	Uncertain significance (Jul 27, 2024)
11-2269935-G-T		not specified	Uncertain significance (Jul 14, 2021)
11-2269962-G-C		not specified	Uncertain significance (Sep 20, 2023)
11-2270068-C-G		not specified	Uncertain significance (Dec 19, 2022)
11-2270096-G-T		not specified	Uncertain significance (Dec 21, 2022)
11-2270101-G-A		not specified	Uncertain significance (Jan 23, 2024)
11-2270105-G-C		not specified	Uncertain significance (Nov 11, 2024)
11-2270184-G-C		not specified	Uncertain significance (Nov 21, 2024)
11-2270196-C-G		not specified	Uncertain significance (Mar 24, 2023)
11-2270199-G-A		not specified	Uncertain significance (Mar 21, 2022)
11-2270228-G-T		not specified	Uncertain significance (Apr 22, 2024)
11-2270256-G-C		not specified	Uncertain significance (Feb 23, 2023)
11-2270272-C-T		not specified	Uncertain significance (Aug 12, 2021)
11-2270281-C-T		not specified	Uncertain significance (Dec 27, 2023)
11-2270284-G-T		not specified	Uncertain significance (Jul 09, 2021)
11-2270302-G-T		not specified	Uncertain significance (Jul 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ASCL2	protein_coding	protein_coding	ENST00000331289	1	2458

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.346	0.496	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.556	32	42.2	0.759	0.00000214	1135
Missense in Polyphen		17	25.991	0.65408		530
Synonymous	1.11	14	20.4	0.686	0.00000104	460
Loss of Function	0.710	0	0.586	0.00	2.45e-8	11

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: AS-C proteins are involved in the determination of the neuronal precursors in the peripheral nervous system and the central nervous system.

Recessive Scores

• pRec: 0.0997

Haploinsufficiency Scores

• pHI: 0.375
• hipred: N
• hipred_score: 0.285
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.974

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ascl2
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; digestive/alimentary phenotype; normal 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;response to hypoxia;placenta development;transcription, DNA-templated;regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;sensory organ development;negative regulation of Schwann cell proliferation;neuron differentiation;somatic stem cell population maintenance;positive regulation of transcription by RNA polymerase II;regulation of neurogenesis;spongiotrophoblast differentiation;spongiotrophoblast layer development
• Cellular component: nucleus;cytoplasm;RNA polymerase II transcription factor complex
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;transcription factor binding;protein dimerization activity;E-box binding