Is BLTP1 p.Thr3862Pro (c.11584A>C) pathogenic?

BLTP1 p.Thr3862Pro (c.11584A>C) is classified Uncertain significance in BLTP1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-11-09). AlphaMissense: likely benign (0.0936); Ultra-rare (popmax 0.0156%, eas).

How common is BLTP1 p.Thr3862Pro (c.11584A>C) in the general population?

BLTP1 p.Thr3862Pro (c.11584A>C) is ultra-rare (popmax 0.0156%, eas) (gnomAD).

What do computational predictors say about BLTP1 p.Thr3862Pro (c.11584A>C)?

AlphaMissense predicts likely benign (score 0.0936) — an in-silico prediction, not a clinical call.

BLTP1 p.Thr3862Pro

c.11584A>C · VCV3337856

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0936 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0156%, eas)

Computational evidence

Protein change
AlphaMissense	0.0936	likely benign
REVEL	0.337	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.1	GERP -0.14, phastCons 0.85
Regional constraint	o/e 0.84	unconstrained · MANE · 12 kb · p 0.0011 · regional, not allelic
Overall
CADD	14.31	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM T3774P vs ClinVar T3862P) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0156% East Asian · 7/44,806 alleles

Filtering AF 0.00727% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00515%

Overall 0.0049% 79/1,612,002 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0156%	6,401
Remaining individualsnot grpmax-eligible	0.00802%	12,470
Admixed American	0.0067%	14,936
South Asian	0.00549%	18,204
European (non-Finnish)	0.00484%	20,682
African / African-American	0.00134%	74,780

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: BLTP1
Protein: p.Thr3862Pro
Coding: c.11584A>C
MANE Select: NM_001384125
Type: single nucleotide variant
Location: chr4:122331396 (GRCh38)
Residue 3862: a UniProt-annotated variant site (in alkkucs)

Full BLTP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BLTP1 p.Arg968Cys Likely pathogenic ★★ ⚠ same type
BLTP1 c.1498+4A>G Uncertain significance ★★ same type
BLTP1 p.Ala2332Thr Uncertain significance ★★ ⚠ same type
BLTP1 p.Arg1317His Uncertain significance ★★ same type
BLTP1 p.Arg1791Lys Uncertain significance ★★ ⚠ same type
BLTP1 p.Arg2095His Uncertain significance ★★ same type
BLTP1 p.Arg2279Cys Uncertain significance ★★ same type
BLTP1 p.Arg3665Gln 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/bltp1-p-thr3862pro (accessed [today's date]).

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