BCAS4

breast carcinoma amplified sequence 4

Basic information

Region (hg38): 20:50794893-50877177

Links

ENSG00000124243 ∙ NCBI:55653 ∙ OMIM:607471 ∙ HGNC:14367 ∙ Uniprot:Q8TDM0 ∙ 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 BCAS4 gene.

• Inborn genetic diseases (10 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCAS4 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				3		3
missense			7	3	2	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	7	6	2

Variants in BCAS4

This is a list of pathogenic ClinVar variants found in the BCAS4 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-50795000-C-G		not specified	Uncertain significance (May 03, 2023)
20-50795096-G-A		not specified	Likely benign (Dec 07, 2021)
20-50795110-G-A			Likely benign (Jan 03, 2019)
20-50795126-G-A		not specified	Uncertain significance (Sep 12, 2023)
20-50795158-C-T			Likely benign (May 24, 2018)
20-50795168-G-T		not specified	Uncertain significance (Nov 22, 2023)
20-50818212-C-T		not specified	Uncertain significance (Jan 23, 2024)
20-50830276-C-T			Benign (Dec 31, 2019)
20-50830283-G-A		not specified	Uncertain significance (Jan 23, 2023)
20-50830329-G-C		not specified	Uncertain significance (Dec 14, 2022)
20-50841788-A-G		not specified	Uncertain significance (Nov 01, 2022)
20-50841802-C-G		not specified	Uncertain significance (Dec 01, 2022)
20-50841821-A-G		not specified	Uncertain significance (Nov 08, 2022)
20-50841889-T-A			Benign (Dec 31, 2019)
20-50841890-C-A			Benign (Dec 31, 2019)
20-50876068-C-A			Likely benign (Oct 01, 2023)
20-50876491-A-G		not specified	Likely benign (Mar 24, 2023)
20-50876507-G-A		not specified	Uncertain significance (Dec 08, 2023)
20-50876511-C-T		not specified	Likely benign (Sep 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCAS4	protein_coding	protein_coding	ENST00000358791	6	82284

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000568	0.471	125704	0	40	125744	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.384	102	114	0.898	0.00000688	1335
Missense in Polyphen		28	30.861	0.90731		408
Synonymous	0.236	43	45.0	0.955	0.00000272	451
Loss of Function	0.415	7	8.29	0.844	4.35e-7	98

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000601	0.000601
European (Non-Finnish)	0.000224	0.000220
Middle Eastern	0.00	0.00
South Asian	0.0000337	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0949

Haploinsufficiency Scores

• pHI: 0.146
• hipred: N
• hipred_score: 0.123
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.469

Gene Damage Prediction

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

Gene ontology

• Cellular component: BLOC-1 complex