Is BLTP1 p.Ile55= (c.165T>C) pathogenic?

BLTP1 p.Ile55= (c.165T>C) is classified Likely benign in BLTP1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-01-28). Absent from gnomAD v4.1; Associated with BLTP1-related disorder.

What condition is associated with BLTP1 p.Ile55= (c.165T>C)?

BLTP1 p.Ile55= (c.165T>C) is associated with BLTP1-related disorder (ClinVar).

How common is BLTP1 p.Ile55= (c.165T>C) in the general population?

BLTP1 p.Ile55= (c.165T>C) is absent from gnomAD v4.1 (gnomAD).

BLTP1 p.Ile55=

c.165T>C · rs2479139410 · VCV3044913

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 2.7	GERP 2.2, phastCons 1
Overall
CADD	12.08	PHRED · no single calibrated threshold — expert panels disagree

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.Ile55=
Coding: c.165T>C
MANE Select: NM_001384125
dbSNP: rs2479139410
Type: single nucleotide variant
Location: chr4:122173103 (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-ile55 (accessed [today's date]).

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