BCAS3

Chr 17AR

BCAS3 microtubule associated cell migration factor

Also known as: GAOB1, HEMARS, MAAB, PHAF2

NCBI Gene: 54828 ENSG00000141376 UniProt: Q9H6U6 OMIM: 607470

BCAS3 encodes a protein that regulates cell polarity and directional migration through CDC42 activation and actin cytoskeleton reorganization, functions as a transcriptional coactivator for estrogen-responsive genes, and plays a regulatory role in autophagy. Mutations cause Hengel-Maroofian-Schols syndrome with autosomal recessive inheritance. The gene is highly constrained against loss-of-function variants (LOEUF 0.467), indicating that complete loss of protein function is likely detrimental.

OMIM ResearchSummary from RefSeq, UniProt

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]

OMIM ResearchGenerating clinical summary…

LOFmechanismARLOEUF 0.471 OMIM phenotype

Clinical Summary— BCAS3

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Population Constraint (gnomAD)

Constrained for loss-of-function variants (OE-LoF 0.31) despite low pLI — interpret in context.

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ClinVar Variants

18 unique Pathogenic / Likely Pathogenic· 118 VUS of 174 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

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?

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?

LoF OE?0.31 (0.22–0.47)

0≤0.351.4

Missense OE?0.69 (0.63–0.75)

0≤0.61.4

Synonymous OE?0.98

0≤1.21.6

LoF obs/exp: 18 / 57.2Missense obs/exp: 375 / 546.0Syn Z: 0.23

ClinVar Variant Classifications

174 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic1

Likely Pathogenic17

VUS118

Likely Benign9

Benign2

Pathogenic

Likely Pathogenic

118

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	1	0	0	0	1
Likely Pathogenic	12	4	1	0	17
VUS	1	116	1	0	118
Likely Benign	0	3	2	4	9
Benign	0	1	0	1	2
Total	14	124	4	5	147

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

View in ClinVar →

22 pathogenic / likely-pathogenic (of 40) ClinVar copy-number / structural variants overlap BCAS3 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →