BCAS3

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

Basic information

Region (hg38): 17:60677452-61392838

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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hengel-Maroofian-Schols syndrome	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	34022130

ClinVar

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

• Inborn genetic diseases (38 variants)
• not provided (5 variants)
• BCAS3-related condition (2 variants)
• Hengel-Maroofian-Schols syndrome (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.

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				1	1	2
missense			41	1		42
nonsense	1	1				2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	1	41	2	1

Variants in BCAS3

This is a list of pathogenic ClinVar variants found in the BCAS3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-60679530-C-T		Global developmental delay • Hengel-Maroofian-Schols syndrome	Pathogenic/Likely pathogenic (Sep 12, 2023)
17-60683995-A-G		Inborn genetic diseases	Uncertain significance (Jan 24, 2024)
17-60689725-A-G		Inborn genetic diseases	Uncertain significance (Mar 08, 2024)
17-60689735-T-C		Inborn genetic diseases	Uncertain significance (Dec 14, 2021)
17-60747213-C-T		Global developmental delay	Likely pathogenic (Jan 12, 2021)
17-60747234-C-T		Inborn genetic diseases	Uncertain significance (Dec 19, 2023)
17-60747235-A-C		Inborn genetic diseases	Uncertain significance (Jun 24, 2022)
17-60747262-T-A		Hengel-Maroofian-Schols syndrome	Likely pathogenic (-)
17-60808006-G-C		Inborn genetic diseases	Uncertain significance (Dec 22, 2023)
17-60868628-AT-A		Global developmental delay	Likely pathogenic (Jan 12, 2021)
17-60868675-C-A		Global developmental delay	Likely pathogenic (Jan 12, 2021)
17-60868682-C-T		Inborn genetic diseases	Uncertain significance (May 18, 2022)
17-60874669-G-T		Inborn genetic diseases	Uncertain significance (Dec 13, 2022)
17-60889701-A-G		Inborn genetic diseases	Uncertain significance (Jan 19, 2022)
17-60889730-A-G		Inborn genetic diseases	Likely benign (Jul 11, 2023)
17-60889745-C-T		Inborn genetic diseases	Uncertain significance (Aug 30, 2021)
17-60889759-T-G		Global developmental delay • Hengel-Maroofian-Schols syndrome	Pathogenic/Likely pathogenic (Sep 12, 2023)
17-60902642-G-A		Inborn genetic diseases	Uncertain significance (Dec 02, 2022)
17-60910599-G-A		Inborn genetic diseases	Uncertain significance (Mar 27, 2023)
17-60910613-G-A		Inborn genetic diseases	Uncertain significance (May 27, 2022)
17-60910614-A-C		Inborn genetic diseases	Uncertain significance (Nov 03, 2022)
17-60910620-C-T		Inborn genetic diseases	Uncertain significance (Jan 31, 2023)
17-60910629-G-A		Inborn genetic diseases	Uncertain significance (Oct 05, 2023)
17-60910640-C-T		Inborn genetic diseases	Uncertain significance (Jan 04, 2022)
17-60924424-T-G		Inborn genetic diseases	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCAS3	protein_coding	protein_coding	ENST00000390652	24	715386

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000138	1.00	124771	0	37	124808	0.000148

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.60	375	546	0.687	0.0000307	6050
Missense in Polyphen		153	224.41	0.68178		2416
Synonymous	0.226	192	196	0.979	0.0000114	1840
Loss of Function	4.80	18	57.2	0.315	0.00000358	574

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000449	0.000449
Ashkenazi Jewish	0.000200	0.000199
East Asian	0.000167	0.000167
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000107	0.000106
Middle Eastern	0.000167	0.000167
South Asian	0.0000988	0.0000980
Other	0.000165	0.000165

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

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

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