Is BCAS3 p.Gly159= (c.477C>T) pathogenic?

BCAS3 p.Gly159= (c.477C>T) is classified Likely benign in BCAS3 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-05-01). Ultra-rare (popmax 0.0366%, amr); Associated with Inborn genetic diseases.

What condition is associated with BCAS3 p.Gly159= (c.477C>T)?

BCAS3 p.Gly159= (c.477C>T) is associated with Inborn genetic diseases (ClinVar).

How common is BCAS3 p.Gly159= (c.477C>T) in the general population?

BCAS3 p.Gly159= (c.477C>T) is ultra-rare (popmax 0.0366%, amr) (gnomAD).

BCAS3 p.Gly159=

c.477C>T · VCV3480033

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0366%, amr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.19	GERP -5.2, phastCons 0.29
Overall
CADD	10.09	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0366% Admixed American · 15/40,996 alleles

Filtering AF 0.0225% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0182%

Overall 0.00105% 16/1,525,650 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0366%	2,733
European (non-Finnish)	8.73e-05%	1,144,831

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: BCAS3
Protein: p.Gly159=
Coding: c.477C>T
MANE Select: NM_017679
Type: single nucleotide variant
Location: chr17:60868576 (GRCh38)
Gene constraint: LOEUF 0.58 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 65.25
Residue 159: a UniProt-annotated variant site (in hemars)

Full BCAS3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BCAS3 p.Ala349Val Uncertain significance ★★ ⚠ same condition
BCAS3 p.Arg254Cys Uncertain significance ★★ ⚠ same condition
BCAS3 p.Asp337Glu Uncertain significance ★★ ⚠ same condition
BCAS3 p.Pro755Leu Uncertain significance ★★ ⚠ same condition
BCAS3 c.1638-7789T>C Uncertain significance ★ ⚠ same condition
BCAS3 c.661+6T>C Uncertain significance ★ same condition
BCAS3 p.Ala125Val Uncertain significance ★ ⚠ same condition
BCAS3 p.Ala136Pro Uncertain significance ★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/bcas3-p-gly159 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown