BCAS3

Chr 17AR

BCAS3 microtubule associated cell migration factor

Also known as: GAOB1, HEMARS, MAAB, PHAF2

NCBI Gene: 54828ENSG00000141376UniProt: Q9H6U6

Enables several functions, including acetyltransferase activator activity; beta-tubulin binding activity; and histone acetyltransferase binding activity. Involved in cellular response to estrogen stimulus; positive regulation of catalytic activity; and positive regulation of transcription by RNA polymerase II. Located in euchromatin; nucleus; and phagophore assembly site. Implicated in Hengel-Maroofian-Schols syndrome. Biomarker of breast cancer. [provided by Alliance of Genome Resources, Jul 2025]

Primary Disease Associations & Inheritance

Hengel-Maroofian-Schols syndromeMIM #619641
AR
182
ClinVar variants
39
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— BCAS3
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.31) despite low pLI — interpret in context.
📋
ClinVar Variants
39 Pathogenic / Likely Pathogenic· 131 VUS of 182 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.47LOEUF
pLI 0.000
Z-score 4.80
OE 0.31 (0.22–0.47)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
2.60Z-score
OE missense 0.69 (0.63–0.75)
375 obs / 546.0 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.31 (0.22–0.47)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.69 (0.63–0.75)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.98
0≤1.21.6
LoF obs/exp: 18 / 57.2Missense obs/exp: 375 / 546.0Syn Z: 0.23

ClinVar Variant Classifications

182 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic18
Likely Pathogenic21
VUS131
Likely Benign10
Benign2
18
Pathogenic
21
Likely Pathogenic
131
VUS
10
Likely Benign
2
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
18
0
18
Likely Pathogenic
3
4
14
0
21
VUS
0
114
17
0
131
Likely Benign
0
3
3
4
10
Benign
0
1
0
1
2
Total3122525182

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

BCAS3 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Gene2Phenotype Curations

BCAS3-related neurodevelopmental disorder with thinning of corpus callosum and cerebellar atrophy

strong
ARLoss Of FunctionAbsent Gene Product
Dev. Disorders
G2P ↗

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM

Hengel-Maroofian-Schols syndrome

MIM #619641

Molecular basis of disorder known

Autosomal recessive
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
BCAS3 exhibits oncogenic properties by promoting CRL4A-mediated ubiquitination of p53 in breast cancer.
Zhou Z et al.·Cell Prolif
2021
Genome-Wide Association Study for eGFR in a Taiwanese Population.
Chen YC et al.·Clin J Am Soc Nephrol
2022Meta-analysis
Bi-allelic loss-of-function variants in BCAS3 cause a syndromic neurodevelopmental disorder.
Hengel H et al.·Am J Hum Genet
2021Case report
Common variant of BCAS3 is associated with gout risk in Japanese population: the first replication study after gout GWAS in Han Chinese.
Sakiyama M et al.·BMC Med Genet
2018
Generalization of associations of kidney-related genetic loci to American Indians.
Franceschini N et al.·Clin J Am Soc Nephrol
2014
Whole exome sequencing identifies multiple novel candidate genes in familial gastroschisis.
Salinas-Torres VM et al.·Mol Genet Genomic Med
2020
RWCFusion: identifying phenotype-specific cancer driver gene fusions based on fusion pair random walk scoring method.
Zhao J et al.·Oncotarget
2016
An Integrated Transcriptomics and Genomics Approach Detects an X/Autosome Translocation in a Female with Duchenne Muscular Dystrophy.
Segarra-Casas A et al.·Int J Mol Sci
2024Case report
Plasma Vitamin C and Type 2 Diabetes: Genome-Wide Association Study and Mendelian Randomization Analysis in European Populations.
Zheng JS et al.·Diabetes Care
2021
Identification of novel genetic susceptibility loci for calcium-containing kidney stone disease by genome-wide association study and polygenic risk score in a Taiwanese population.
Chen WC et al.·Urolithiasis
2024
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools