Is BLTP1 p.Pro3798Leu (c.11393C>T) pathogenic?

BLTP1 p.Pro3798Leu (c.11393C>T) is classified Likely benign in BLTP1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-01). AlphaMissense: likely benign (0.0949); Rare (popmax 0.145%, nfe).

How common is BLTP1 p.Pro3798Leu (c.11393C>T) in the general population?

BLTP1 p.Pro3798Leu (c.11393C>T) is rare (popmax 0.145%, nfe) (gnomAD).

What do computational predictors say about BLTP1 p.Pro3798Leu (c.11393C>T)?

AlphaMissense predicts likely benign (score 0.0949) — an in-silico prediction, not a clinical call.

BLTP1 p.Pro3798Leu

c.11393C>T · rs75040092 · VCV2655067

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.0949 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.145%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Computational evidence

Protein change
AlphaMissense	0.0949	likely benign
REVEL	0.117	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.8	GERP 0.86, phastCons 1
Regional constraint	o/e 0.84	unconstrained · MANE · 12 kb · p 0.0011 · regional, not allelic
Overall
CADD	20.6	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 P3710L vs ClinVar P3798L) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.145% European (non-Finnish) · 1,704/1,178,162 alleles

Filtering AF 0.139% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.137%

Overall 0.12% 1,929/1,611,192 alleles · rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.15%	666
European (non-Finnish)grpmax	0.145%	691
Ashkenazi Jewishnot grpmax-eligible	0.132%	756
Remaining individualsnot grpmax-eligible	0.0946%	1,057
Middle Eastern	0.0331%	3,022
Admixed American	0.0218%	4,592
African / African-American	0.0214%	4,673

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Pro3798Leu
Coding: c.11393C>T
MANE Select: NM_001384125
dbSNP: rs75040092
Type: single nucleotide variant
Location: chr4:122328237 (GRCh38)
Residue 3798: 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-pro3798leu (accessed [today's date]).

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