BCAS1

protein-coding

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

Gene summary

This gene resides in a region at 20q13 which is amplified in a variety of tumor types and associated with more aggressive tumor phenotypes. Among the genes identified from this region, it was found to be highly expressed in three amplified breast cancer cell lines and in one breast tumor without amplification at 20q13.2. However, this gene is not in the common region of maximal amplification and its expression was not detected in the breast cancer cell line MCF7, in which this region is highly amplified. Although not consistently expressed, this gene is a candidate oncogene. [provided by RefSeq, Apr 2016]

MANE transcript

NM_001366298.2

Inheritance

—

ClinVar variants

U:72B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.55

Max pathogenic AF

—

Genomic locus

chr20:53,936,777-54,070,594

External References & Databases

Ensembl (ENSG00000064787)

Transcript & Mutation Effects

hg38 • Region Span ~133.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BCAS1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 76

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001366298.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar		3 clinvar	5
missense			68 clinvar	9 clinvar	2 clinvar	79
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	72	9	5	86

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 59 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001366298.2	RefSeq	NP_001353227.1	12	MANE Select
ENST00000688948.1	Ensembl	ENSP00000508731.1	12	MANE Select
NM_001316361.3	RefSeq	NP_001303290.1	9	Standard
NM_001323347.2	RefSeq	NP_001310276.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

myelination

Cellular Component

cytoplasm
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000395961
Coding exons: 11
Length: 133989
Individuals with no LoFs: 125619
Homozygous LoFs: 0
Heterozygous LoFs: 129
Defined: 125748
p: 0.000513

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.250	337	324	1.04	0.0000178	3794
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00049	0.00049	rare
Latino/Admixed American	0.00095	0.00095	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00064	0.00063	rare
South Asian	0.00030	0.00029	rare
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.948

Gene Damage Prediction

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