Is LIPC p.Val155= (c.465G>T) pathogenic?

LIPC p.Val155= (c.465G>T) is classified Benign in LIPC (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-02-04). Common (popmax 58.4%, nfe) — too common for a highly-penetrant pathogenic allele; Associated with hyperlipidemia due to hepatic triglyceride lipase deficiency.

What condition is associated with LIPC p.Val155= (c.465G>T)?

LIPC p.Val155= (c.465G>T) is associated with hyperlipidemia due to hepatic triglyceride lipase deficiency (ClinVar).

LIPC p.Val155=

Q: How common is LIPC p.Val155= (c.465G>T) in the general population?

LIPC p.Val155= (c.465G>T) is common (popmax 58.4%, nfe) — too common for a highly-penetrant pathogenic allele (gnomAD).

Q: How is Hyperlipidemia due to hepatic triacylglycerol lipase deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.465G>T · rs690 · VCV316660

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Common

common (popmax 58.4%, nfe) — too common for a highly-penetrant pathogenic allele

Conditions

hyperlipidemia due to hepatic triglyceride lipase deficiency

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 0.48	GERP -7.9
Overall
CADD	0.378	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 58.4% European (non-Finnish) · 684,713/1,172,358 alleles

Filtering AF 58.3% ClinGen BA1/BS1 input FAF95, joint · FAF99 58.2%

Overall 56.4% 905,405/1,605,242 alleles · common exomes 822,296/1,453,260 · genomes 83,109/151,982 · joint denominator

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	72.9%	1
Ashkenazi Jewishnot grpmax-eligible	58.9%	2
European (non-Finnish)grpmax	58.4%	2
South Asian	58.1%	2
Middle Eastern	56.7%	2
Finnishnot grpmax-eligible	55.1%	2
Remaining individualsnot grpmax-eligible	54.9%	2
African / African-American	54.6%	2
Admixed American	43.8%	2
East Asian	22.2%	5

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: LIPC
Protein: p.Val155=
Coding: c.465G>T
MANE Select: NM_000236
dbSNP: rs690
Type: single nucleotide variant
Location: chr15:58542542 (GRCh38)
Gene constraint: LOEUF 1.102 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.03

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

Disease context

hyperlipidemia due to hepatic triglyceride lipase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Hyperlipidemia due to hepatic triacylglycerol lipase deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: No data available

Similar variants

LIPC c.456+2T>C Uncertain significance ★★ same condition
LIPC c.456+5C>T Uncertain significance ★★ same condition
LIPC p.Ala105Val Uncertain significance ★★ ⚠ same condition
LIPC p.Ala106Val Uncertain significance ★★ ⚠ same condition
LIPC p.Arg135Cys Uncertain significance ★★ ⚠ same condition
LIPC p.Arg225Gln Uncertain significance ★★ ⚠ same condition
LIPC p.Arg329His Uncertain significance ★★ ⚠ same condition
LIPC p.Arg333Gln 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/lipc-p-val155 (accessed [today's date]).

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