Is BLTP1 p.Val4647= (c.13941A>G) pathogenic?

BLTP1 p.Val4647= (c.13941A>G) is classified Likely benign in BLTP1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-09-23). Ultra-rare (popmax 0.045%, amr); Associated with BLTP1-related disorder.

What condition is associated with BLTP1 p.Val4647= (c.13941A>G)?

BLTP1 p.Val4647= (c.13941A>G) is associated with BLTP1-related disorder (ClinVar).

How common is BLTP1 p.Val4647= (c.13941A>G) in the general population?

BLTP1 p.Val4647= (c.13941A>G) is ultra-rare (popmax 0.045%, amr) (gnomAD).

BLTP1 p.Val4647=

c.13941A>G · rs756805280 · VCV3040334

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.045%, amr)

Conditions

BLTP1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.98	GERP 0.53, phastCons 0.99
Overall
CADD	3.501	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.045% Admixed American · 27/59,976 alleles

Filtering AF 0.0317% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0273%

Overall 0.00167% 27/1,613,602 alleles · ultra-rare exomes 24/1,461,462 · genomes 3/152,140 · joint denominator

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.Val4647=
Coding: c.13941A>G
MANE Select: NM_001384125
dbSNP: rs756805280
Type: single nucleotide variant
Location: chr4:122349902 (GRCh38)
Residue 4647: 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.Val4647Ile Uncertain significance ★ same residue
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.Phe3799Ser Uncertain significance ★ 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-val4647 (accessed [today's date]).

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