Is BLTP1 p.Lys5= (c.15G>A) pathogenic?

BLTP1 p.Lys5= (c.15G>A) is classified Likely benign in BLTP1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-15). Ultra-rare (popmax 0.0385%, afr); Associated with BLTP1-related disorder.

What condition is associated with BLTP1 p.Lys5= (c.15G>A)?

BLTP1 p.Lys5= (c.15G>A) is associated with BLTP1-related disorder (ClinVar).

How common is BLTP1 p.Lys5= (c.15G>A) in the general population?

BLTP1 p.Lys5= (c.15G>A) is ultra-rare (popmax 0.0385%, afr) (gnomAD).

BLTP1 p.Lys5=

c.15G>A · rs147412676 · VCV3041193

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0385%, afr)

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 1.4	GERP -0.85, phastCons 1
Overall
CADD	7.893	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0385% African / African-American · 28/72,782 alleles

Filtering AF 0.0273% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0236%

Overall 0.00203% 32/1,574,770 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0385%	2,599
Remaining individualsnot grpmax-eligible	0.00328%	30,494
Admixed American	0.00183%	54,510
European (non-Finnish)	8.62e-05%	1,159,938

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.Lys5=
Coding: c.15G>A
MANE Select: NM_001384125
dbSNP: rs147412676
Type: single nucleotide variant
Location: chr4:122170662 (GRCh38)

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.Phe3799Ser Uncertain significance ★ same condition
BLTP1 p.Val1878Ala 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-lys5 (accessed [today's date]).

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