Is BLTP1 p.Asp1835fs (c.5499del) pathogenic?

BLTP1 p.Asp1835fs (c.5499del) is classified Pathogenic in BLTP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-10-23). Absent from gnomAD.

How common is BLTP1 p.Asp1835fs (c.5499del) in the general population?

BLTP1 p.Asp1835fs (c.5499del) is absent from gnomAD (gnomAD).

BLTP1 p.Asp1835fs

c.5499del · rs1762121275 · VCV987176

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 35 of 88
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 2.8, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BLTP1
Protein: p.Asp1835fs
Coding: c.5499del
MANE Select: NM_001384125
dbSNP: rs1762121275
Type: Deletion
Location: chr4:122247344 (GRCh38)
Residue 1835: 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.Arg1832fs Pathogenic ★ same type
BLTP1 p.Arg2623fs Likely pathogenic ★ same type
BLTP1 p.Glu586fs Pathogenic ★ same type
BLTP1 p.His1088fs Pathogenic ★ same type
BLTP1 p.Phe231fs Likely pathogenic ★ same type
BLTP1 p.Thr4470fs Pathogenic ★ same type
BLTP1 p.Val3052fs Pathogenic ★ same type
BLTP1 p.Val83fs Pathogenic ★ 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-asp1835fs (accessed [today's date]).

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