GeneBe

BCAS3

BCAS3 microtubule associated cell migration factor, the group of WD repeat domain containing

Basic information

Region (hg38): 17:60677453-61392838

Links

ENSG00000141376 ∙ NCBI:54828 ∙ OMIM:607470 ∙ HGNC:14347 ∙ Uniprot:Q9H6U6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • Hengel-Maroofian-Schols syndrome (Strong), mode of inheritance: AR
  • Hengel-Maroofian-Schols syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Hengel-Maroofian-Schols syndromeARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Musculoskeletal; Neurologic; Ophthalmologic34022130

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BCAS3 gene.

  • Inborn_genetic_diseases (103 variants)
  • Global_developmental_delay (12 variants)
  • Hengel-Maroofian-Schols_syndrome (9 variants)
  • not_provided (9 variants)
  • BCAS3-related_disorder (2 variants)
  • not_specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCAS3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017679.5. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
1
clinvar
 5
missense
4
clinvar
101
clinvar
3
clinvar
1
clinvar
 109
nonsense
1
clinvar
8
clinvar
 9
start loss
0
frameshift
2
clinvar
 2
splice donor/acceptor (+/-2bp)
1
clinvar
 1
Total 1 14 102 7 2

Highest pathogenic variant AF is 0.000024247489

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
BCAS3protein_codingprotein_codingENST00000390652 24715386
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.0001381.001247710371248080.000148
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.603755460.6870.00003076050
Missense in Polyphen153224.410.681782416
Synonymous0.2261921960.9790.00001141840
Loss of Function4.801857.20.3150.00000358574

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004490.000449
Ashkenazi Jewish0.0002000.000199
East Asian0.0001670.000167
Finnish0.0001390.000139
European (Non-Finnish)0.0001070.000106
Middle Eastern0.0001670.000167
South Asian0.00009880.0000980
Other0.0001650.000165

dbNSFP

Source: dbNSFP

Function
FUNCTION: Plays a role in angiogenesis. Participates in the regulation of cell polarity and directional endothelial cell migration by mediating both the activation and recruitment of CDC42 and the reorganization of the actin cytoskeleton at the cell leading edge. Promotes filipodia formation (By similarity). Functions synergistically with PELP1 as a transcriptional coactivator of estrogen receptor-responsive genes. Stimulates histone acetyltransferase activity. Binds to chromatin. {ECO:0000250|UniProtKB:Q8CCN5, ECO:0000269|PubMed:17505058}.;
Disease
DISEASE: Note=A chromosomal aberration involving BCAS3 has been found in some breast carcinoma cell lines. Translocation t(17;20)(q23;q13) with BCAS4.;
Pathway
Ectoderm Differentiation (Consensus)

Intolerance Scores

loftool
0.479
rvis_EVS
-0.75
rvis_percentile_EVS
13.67

Haploinsufficiency Scores

pHI
0.637
hipred
Y
hipred_score
0.682
ghis
0.537

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.948

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Bcas3
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); growth/size/body region phenotype; 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
angiogenesis;Golgi organization;positive regulation of endothelial cell migration;microtubule organizing center organization;negative regulation of GTPase activity;tube formation;response to starvation;positive regulation of catalytic activity;positive regulation of GTPase activity;positive regulation of transcription by RNA polymerase II;positive regulation of filopodium assembly;negative regulation of focal adhesion assembly;cellular response to estrogen stimulus;positive regulation of intracellular protein transport;activation of GTPase activity;regulation of establishment of cell polarity;positive regulation of actin cytoskeleton reorganization
Cellular component
nucleus;nucleolus;cytoplasm;cytoplasmic microtubule;cell leading edge;transcriptionally active chromatin;intermediate filament cytoskeleton;cell periphery
Molecular function
chromatin binding;protein binding;transcription factor binding;acetyltransferase activator activity;histone acetyltransferase binding;nuclear hormone receptor binding;histone binding;beta-tubulin binding