Is BLTP3A p.Arg829Ser (c.2487G>C) pathogenic?

BLTP3A p.Arg829Ser (c.2487G>C) is classified Uncertain significance in BLTP3A (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-02). AlphaMissense: ambiguous (0.4528); Ultra-rare (popmax 0.0333%, afr).

How common is BLTP3A p.Arg829Ser (c.2487G>C) in the general population?

BLTP3A p.Arg829Ser (c.2487G>C) is ultra-rare (popmax 0.0333%, afr) (gnomAD).

What do computational predictors say about BLTP3A p.Arg829Ser (c.2487G>C)?

AlphaMissense predicts ambiguous (score 0.4528) — an in-silico prediction, not a clinical call.

BLTP3A p.Arg829Ser

c.2487G>C · rs534091968 · VCV3134345

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4528 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0333%, afr)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Computational evidence

Protein change
AlphaMissense	0.4528	ambiguous
REVEL	0.228	benign-leaning
SaProt	LLR -5.78	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.2	GERP -2.8, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 80 kb · p 4.8e-07 · regional, not allelic
Overall
CADD	17.23	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0333% African / African-American · 25/75,040 alleles

Filtering AF 0.0231% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0197%

Overall 0.00186% 30/1,614,164 alleles · ultra-rare exomes 13/1,461,854 · genomes 17/152,310 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0333%	3,002
Admixed American	0.005%	20,007
European (non-Finnish)	0.000169%	590,023

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: BLTP3A
Protein: p.Arg829Ser
Coding: c.2487G>C
MANE Select: NM_017754
dbSNP: rs534091968
Type: single nucleotide variant
Location: chr6:34858843 (GRCh38)
Structure: AlphaFold pLDDT 67.37

Full BLTP3A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BLTP3A p.Val1190Phe Uncertain significance ★★ ⚠ same type
BLTP3A p.Ala1021Gly Uncertain significance ★ ⚠ same type
BLTP3A p.Ala1174Pro Uncertain significance ★ ⚠ same type
BLTP3A p.Ala1217Val Uncertain significance ★ ⚠ same type
BLTP3A p.Ala1366Ser Uncertain significance ★ ⚠ same type
BLTP3A p.Ala257Thr Uncertain significance ★ ⚠ same type
BLTP3A p.Ala263Ser Uncertain significance ★ ⚠ same type
BLTP3A p.Ala373Ser Uncertain significance ★ ⚠ same type

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/bltp3a-p-arg829ser (accessed [today's date]).

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