ASCL4

achaete-scute family bHLH transcription factor 4, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 12:107774704-107776644

Links

ENSG00000187855 ∙ NCBI:121549 ∙ OMIM:609155 ∙ HGNC:24311 ∙ Uniprot:Q6XD76 ∙ 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 ASCL4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ASCL4 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in ASCL4

This is a list of pathogenic ClinVar variants found in the ASCL4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-107775228-C-A		not specified	Uncertain significance (Jul 25, 2024)
12-107775254-G-T		not specified	Uncertain significance (Mar 22, 2023)
12-107775285-G-C		not specified	Uncertain significance (Mar 11, 2024)
12-107775292-G-A		not specified	Uncertain significance (Dec 18, 2023)
12-107775313-G-A		not specified	Uncertain significance (Sep 16, 2021)
12-107775369-C-T		not specified	Uncertain significance (Aug 20, 2024)
12-107775391-G-T		not specified	Uncertain significance (Sep 10, 2024)
12-107775408-C-T		not specified	Uncertain significance (Nov 10, 2022)
12-107775420-G-A		not specified	Uncertain significance (Nov 28, 2024)
12-107775439-T-C		not specified	Uncertain significance (Dec 05, 2024)
12-107775457-G-T		not specified	Uncertain significance (Oct 02, 2023)
12-107775493-A-G		not specified	Uncertain significance (Jan 14, 2025)
12-107775516-C-A		not specified	Uncertain significance (Jul 14, 2021)
12-107775561-C-T		not specified	Uncertain significance (Sep 29, 2023)
12-107775571-T-C		not specified	Uncertain significance (Mar 15, 2024)
12-107775592-A-G		not specified	Uncertain significance (Aug 01, 2024)
12-107775675-G-C		not specified	Uncertain significance (Aug 05, 2024)
12-107775676-G-A		not specified	Uncertain significance (Feb 05, 2024)
12-107775685-A-G		not specified	Uncertain significance (Mar 17, 2023)
12-107775691-C-T		not specified	Uncertain significance (Nov 21, 2023)
12-107775720-G-C		not specified	Uncertain significance (Dec 03, 2024)
12-107775725-G-T		not specified	Uncertain significance (May 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ASCL4	protein_coding	protein_coding	ENST00000342331	1	2260

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00163	0.475	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.04	120	91.9	1.31	0.00000435	1052
Missense in Polyphen		42	29.512	1.4231		358
Synonymous	-0.537	48	43.5	1.10	0.00000204	376
Loss of Function	0.00876	4	4.02	0.995	1.76e-7	45

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: Could be a transcriptional regulator involved in skin development. {ECO:0000269|PubMed:15475265}.

Recessive Scores

• pRec: 0.0879

Haploinsufficiency Scores

• pHI: 0.0800
• hipred: N
• hipred_score: 0.220

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ascl4

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;skin development;positive regulation of transcription by RNA polymerase II
• Cellular component: 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 factor activity;protein binding;transcription factor binding;protein dimerization activity