Is BLTP1 p.Phe3799Ser (c.11396T>C) pathogenic?

BLTP1 p.Phe3799Ser (c.11396T>C) is classified Uncertain significance in BLTP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-27). AlphaMissense: likely benign (0.1978); Absent from gnomAD v4.1; Associated with BLTP1-related disorder.

What condition is associated with BLTP1 p.Phe3799Ser (c.11396T>C)?

BLTP1 p.Phe3799Ser (c.11396T>C) is associated with BLTP1-related disorder (ClinVar).

How common is BLTP1 p.Phe3799Ser (c.11396T>C) in the general population?

BLTP1 p.Phe3799Ser (c.11396T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BLTP1 p.Phe3799Ser (c.11396T>C)?

AlphaMissense predicts likely benign (score 0.1978) — an in-silico prediction, not a clinical call.

BLTP1 p.Phe3799Ser

c.11396T>C · rs2482740668 · VCV2629793

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1978 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

BLTP1-related disorder

Computational evidence

Protein change
AlphaMissense	0.1978	likely benign
REVEL	0.503	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.1	GERP 1.8, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 12 kb · p 0.0011 · regional, not allelic
Overall
CADD	20.4	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 F3711S vs ClinVar F3799S) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: BLTP1
Protein: p.Phe3799Ser
Coding: c.11396T>C
MANE Select: NM_001384125
dbSNP: rs2482740668
Type: single nucleotide variant
Location: chr4:122328240 (GRCh38)
Residue 3799: a UniProt-annotated variant site (in alkkucs)

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

Disease context

BLTP1-related disorder

Similar variants

BLTP1 p.Arg968Cys Likely pathogenic ★★ ⚠ same condition
BLTP1 p.His3063Arg Uncertain significance ★★ same condition
BLTP1 c.10312+2T>C Likely pathogenic ★ same condition
BLTP1 c.11513+1G>C Likely pathogenic ★ same condition
BLTP1 c.5184+1G>T Likely pathogenic ★ same condition
BLTP1 p.Arg3190Ter Likely pathogenic ★ same condition
BLTP1 p.Val1878Ala Uncertain significance ⚠ same condition
BLTP1 c.6378+10T>C 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/bltp1-p-phe3799ser (accessed [today's date]).

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