ASCL3

achaete-scute family bHLH transcription factor 3, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 11:8937577-8943016

Links

ENSG00000176009 ∙ NCBI:56676 ∙ OMIM:609154 ∙ HGNC:740 ∙ Uniprot:Q9NQ33 ∙ 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 ASCL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ASCL3 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			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 ASCL3

This is a list of pathogenic ClinVar variants found in the ASCL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-8937786-C-G		not specified	Uncertain significance (Aug 14, 2023)
11-8937813-G-A		not specified	Uncertain significance (Jun 30, 2023)
11-8937824-T-G		not specified	Uncertain significance (Jun 06, 2023)
11-8937848-C-T		not specified	Uncertain significance (Oct 10, 2023)
11-8937861-G-A		not specified	Uncertain significance (Nov 22, 2023)
11-8937875-C-T		not specified	Uncertain significance (Feb 28, 2024)
11-8937891-C-T		not specified	Uncertain significance (Mar 29, 2022)
11-8937981-C-T		not specified	Uncertain significance (Jan 27, 2022)
11-8937982-G-C		not specified	Uncertain significance (Jun 02, 2024)
11-8938047-C-T		not specified	Uncertain significance (Dec 14, 2021)
11-8938061-A-G		not specified	Uncertain significance (Apr 04, 2023)
11-8938067-T-C		not specified	Uncertain significance (Aug 22, 2023)
11-8938113-A-C		not specified	Uncertain significance (Apr 04, 2024)
11-8938150-G-T		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ASCL3	protein_coding	protein_coding	ENST00000325884	1	5462

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0137	0.686	125529	1	216	125746	0.000863

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.122	105	109	0.967	0.00000626	1176
Missense in Polyphen		34	36.114	0.94146		381
Synonymous	0.703	37	42.9	0.863	0.00000244	371
Loss of Function	0.585	3	4.31	0.696	2.65e-7	53

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00270	0.00270
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00105	0.00104
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000815	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor. Inhibits myogenesis (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0991

Intolerance Scores

• loftool: 0.336
• rvis_EVS: 0.59
• rvis_percentile_EVS: 82.51

Haploinsufficiency Scores

• pHI: 0.602
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.406

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ascl3
• Phenotype: normal phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II
• Cellular component: RNA polymerase II transcription factor complex
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;transcription factor binding;protein dimerization activity