ASCL4

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

Basic information

Region (hg38): 12:107774704-107776644

Links

ENSG00000187855NCBI:121549OMIM:609155HGNC:24311Uniprot:Q6XD76AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
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)3435819
12-107775254-G-T not specified Uncertain significance (Mar 22, 2023)2528145
12-107775285-G-C not specified Uncertain significance (Mar 11, 2024)3130285
12-107775292-G-A not specified Uncertain significance (Dec 18, 2023)3130286
12-107775313-G-A not specified Uncertain significance (Sep 16, 2021)2250573
12-107775369-C-T not specified Uncertain significance (Aug 20, 2024)2391469
12-107775391-G-T not specified Uncertain significance (Sep 10, 2024)3435834
12-107775408-C-T not specified Uncertain significance (Nov 10, 2022)2325266
12-107775420-G-A not specified Uncertain significance (Nov 28, 2024)3435844
12-107775439-T-C not specified Uncertain significance (Dec 05, 2024)3435851
12-107775457-G-T not specified Uncertain significance (Oct 02, 2023)3130281
12-107775493-A-G not specified Uncertain significance (Jan 14, 2025)2364484
12-107775516-C-A not specified Uncertain significance (Jul 14, 2021)2351101
12-107775561-C-T not specified Uncertain significance (Sep 29, 2023)3130282
12-107775571-T-C not specified Uncertain significance (Mar 15, 2024)3317910
12-107775592-A-G not specified Uncertain significance (Aug 01, 2024)3435829
12-107775675-G-C not specified Uncertain significance (Aug 05, 2024)2230560
12-107775676-G-A not specified Uncertain significance (Feb 05, 2024)3130283
12-107775685-A-G not specified Uncertain significance (Mar 17, 2023)2526045
12-107775691-C-T not specified Uncertain significance (Nov 21, 2023)3130284
12-107775720-G-C not specified Uncertain significance (Dec 03, 2024)3435800
12-107775725-G-T not specified Uncertain significance (May 17, 2023)2546987

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ASCL4protein_codingprotein_codingENST00000342331 12260
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.001630.47500000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.0412091.91.310.000004351052
Missense in Polyphen4229.5121.4231358
Synonymous-0.5374843.51.100.00000204376
Loss of Function0.0087644.020.9951.76e-745

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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
ghis

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ascl4
Phenotype

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