BCAS1

brain enriched myelin associated protein 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 20:53936777-54070594

Links

ENSG00000064787 ∙ NCBI:8537 ∙ OMIM:602968 ∙ HGNC:974 ∙ Uniprot:O75363 ∙ 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 BCAS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCAS1 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			28	4	3	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	28	4	7

Variants in BCAS1

This is a list of pathogenic ClinVar variants found in the BCAS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-53944980-A-G		not specified	Likely benign (Jul 19, 2022)
20-53944987-G-A		not specified	Uncertain significance (Jun 07, 2024)
20-53953448-C-T		not specified	Uncertain significance (Oct 03, 2022)
20-53953494-C-G		not specified	Uncertain significance (Jun 11, 2021)
20-53953501-C-G		not specified	Uncertain significance (Dec 21, 2022)
20-53953513-C-T			Benign (Dec 31, 2019)
20-53953573-C-A		not specified	Uncertain significance (May 10, 2024)
20-53953659-C-G		not specified	Uncertain significance (Dec 22, 2023)
20-53953664-G-A		not specified	Uncertain significance (Jan 26, 2022)
20-53953690-T-C			Benign (Mar 30, 2018)
20-53957507-C-T			Benign (Feb 26, 2018)
20-53966922-G-A		not specified	Uncertain significance (Apr 09, 2022)
20-53966998-C-T		not specified	Uncertain significance (Sep 16, 2021)
20-53967004-G-T		not specified	Uncertain significance (Dec 17, 2023)
20-53967067-A-C		not specified	Uncertain significance (Apr 13, 2022)
20-53975403-C-G		not specified	Uncertain significance (Sep 06, 2022)
20-53975430-A-G		not specified	Uncertain significance (Sep 27, 2021)
20-53985340-T-G		not specified	Uncertain significance (Aug 09, 2021)
20-53985463-T-G		not specified	Uncertain significance (May 26, 2023)
20-53985481-T-C		not specified	Likely benign (Mar 02, 2023)
20-53995034-G-C		not specified	Uncertain significance (Jan 16, 2024)
20-53995909-T-C		not specified	Uncertain significance (Jan 26, 2023)
20-53995915-T-C		not specified	Uncertain significance (Dec 06, 2021)
20-53995923-T-C		not specified	Uncertain significance (Apr 05, 2023)
20-53995954-C-T		not specified	Uncertain significance (Feb 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCAS1	protein_coding	protein_coding	ENST00000395961	11	133989

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.95e-7	0.976	125619	0	129	125748	0.000513

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.250	337	324	1.04	0.0000178	3794
Missense in Polyphen		89	85.188	1.0447		1106
Synonymous	0.297	126	130	0.967	0.00000866	1158
Loss of Function	2.10	14	25.4	0.550	0.00000109	345

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00145	0.00145
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000637	0.000633
Middle Eastern	0.0000544	0.0000544
South Asian	0.000298	0.000294
Other	0.000657	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for myelination. {ECO:0000250|UniProtKB:Q80YN3}.

Recessive Scores

• pRec: 0.0891

Intolerance Scores

• loftool: 0.869
• rvis_EVS: 1.47
• rvis_percentile_EVS: 95.28

Haploinsufficiency Scores

• pHI: 0.152
• hipred: N
• hipred_score: 0.270
• ghis: 0.397

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	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Bcas1

Gene ontology

• Biological process: myelination
• Cellular component: cytoplasm;extracellular exosome