Is BLTP1 p.Leu270Phe (c.808C>T) pathogenic?

BLTP1 p.Leu270Phe (c.808C>T) is classified Uncertain significance in BLTP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-09). AlphaMissense: likely benign (0.2741); Very rare (popmax 8.91e-05%, nfe).

How common is BLTP1 p.Leu270Phe (c.808C>T) in the general population?

BLTP1 p.Leu270Phe (c.808C>T) is very rare (popmax 8.91e-05%, nfe) (gnomAD).

What do computational predictors say about BLTP1 p.Leu270Phe (c.808C>T)?

AlphaMissense predicts likely benign (score 0.2741) — an in-silico prediction, not a clinical call.

BLTP1 p.Leu270Phe

c.808C>T · rs1741152009 · VCV1676410

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2741 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.91e-05%, nfe)

Computational evidence

Protein change
AlphaMissense	0.2741	likely benign
REVEL	0.406	indeterminate
Splicing
SpliceAI	Δ0.30	donor loss · deltas
Constraint at this position
Conservation	phyloP 7.7	GERP 1.7, phastCons 1
Regional constraint	o/e 0.82	unconstrained · MANE · 17 kb · p 0.0013 · regional, not allelic
Overall
CADD	22.6	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 8.91e-05% European (non-Finnish) · 1/1,122,556 alleles

Overall 7.45e-05% 1/1,341,678 alleles · very rare

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.Leu270Phe
Coding: c.808C>T
MANE Select: NM_001384125
dbSNP: rs1741152009
Type: single nucleotide variant
Location: chr4:122188075 (GRCh38)

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-leu270phe (accessed [today's date]).

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