Is BCAM p.Ser332= (c.996C>T) pathogenic?

BCAM p.Ser332= (c.996C>T) is classified Likely benign in BCAM (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-06-11). Very rare (popmax 0.0072%, nfe); Associated with BCAM-related disorder.

What condition is associated with BCAM p.Ser332= (c.996C>T)?

BCAM p.Ser332= (c.996C>T) is associated with BCAM-related disorder (ClinVar).

How common is BCAM p.Ser332= (c.996C>T) in the general population?

BCAM p.Ser332= (c.996C>T) is very rare (popmax 0.0072%, nfe) (gnomAD).

BCAM p.Ser332=

c.996C>T · rs375498217 · VCV3033455

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0072%, nfe)

Conditions

BCAM-related disorder

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 -13	GERP -3.5
Overall
CADD	1.411	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0072% European (non-Finnish) · 85/1,180,012 alleles

Filtering AF 0.00596% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00549%

Overall 0.00564% 91/1,613,902 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0072%	13,882
Remaining individualsnot grpmax-eligible	0.0048%	20,828
Finnishnot grpmax-eligible	0.00313%	31,980
African / African-American	0.00134%	74,886

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: BCAM
Protein: p.Ser332=
Coding: c.996C>T
MANE Select: NM_005581
dbSNP: rs375498217
Type: single nucleotide variant
Location: chr19:44814678 (GRCh38)
Gene constraint: LOEUF 1.102 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.29 · 2 PDB
Residue 332: a disulfide bond; the ig-like c2-type 1 domain

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

Disease context

BCAM-related disorder

Similar variants

BCAM p.Ser332Asn Uncertain significance ★ ⚠ same residue
BCAM c.1764-4C>T Likely benign same condition
BCAM c.1882-9G>A Likely benign same condition
BCAM c.433+8T>A Likely benign same condition
BCAM p.Ala238= Benign same condition
BCAM p.Cys237= Benign same condition
BCAM p.Lys451Gln Likely benign same condition
BCAM p.Met204Lys Likely benign 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/bcam-p-ser332 (accessed [today's date]).

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