Is LIPE p.Gln79fs (c.235del) pathogenic?

LIPE p.Gln79fs (c.235del) is classified Pathogenic in LIPE (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-06). Very rare (popmax 0.000678%, nfe); Associated with Lipodystrophy - childhood onset.

What condition is associated with LIPE p.Gln79fs (c.235del)?

LIPE p.Gln79fs (c.235del) is associated with Lipodystrophy - childhood onset (ClinVar).

How common is LIPE p.Gln79fs (c.235del) in the general population?

LIPE p.Gln79fs (c.235del) is very rare (popmax 0.000678%, nfe) (gnomAD).

LIPE p.Gln79fs

c.235del · VCV4682134

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.000678%, nfe)

Conditions

Lipodystrophy - childhood onset

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.41	phastCons 0.35
Overall
CADD	22.9	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000678% European (non-Finnish) · 8/1,180,026 alleles

Filtering AF 0.000292% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000211%

Overall 0.000496% 8/1,614,028 alleles · very rare exomes 6/1,461,894 · genomes 2/152,134 · 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: LIPE
Protein: p.Gln79fs
Coding: c.235del
MANE Select: NM_005357
Type: Deletion
Location: chr19:42426915 (GRCh38)

Full LIPE gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Lipodystrophy - childhood onset

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/lipe-p-gln79fs (accessed [today's date]).

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