Is LIPG p.Val68= (c.204C>T) pathogenic?

LIPG p.Val68= (c.204C>T) is classified Likely benign in LIPG (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-02). Very rare (popmax 0.00666%, amr).

How common is LIPG p.Val68= (c.204C>T) in the general population?

LIPG p.Val68= (c.204C>T) is very rare (popmax 0.00666%, amr) (gnomAD).

LIPG p.Val68=

c.204C>T · rs554682739 · VCV2891737

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00666%, amr)

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 -12	GERP -2.6
Overall
CADD	0.023	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00666% Admixed American · 4/60,022 alleles

Filtering AF 0.00291% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0026%

Overall 0.00359% 58/1,614,206 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00666%	15,006
South Asian	0.00659%	15,180
European (non-Finnish)	0.00381%	26,223
Remaining individualsnot grpmax-eligible	0.0032%	31,256
African / African-American	0.00133%	75,062

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: LIPG
Protein: p.Val68=
Coding: c.204C>T
MANE Select: NM_006033
dbSNP: rs554682739
Type: single nucleotide variant
Location: chr18:49565423 (GRCh38)
Gene constraint: LOEUF 0.883 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.76

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

Similar variants

LIPG p.Val68Phe Uncertain significance ★ ⚠ same residue
LIPG p.Arg112Gly Uncertain significance ★★ ⚠ same type
LIPG p.Arg224Cys Uncertain significance ★★ ⚠ same type
LIPG p.Arg302Cys Uncertain significance ★★ ⚠ same type
LIPG p.Arg431Cys Uncertain significance ★★ ⚠ same type
LIPG p.Arg448His Uncertain significance ★★ ⚠ same type
LIPG p.Arg484Gln Uncertain significance ★★ ⚠ same type
LIPG p.Asn439Ser Uncertain significance ★★ ⚠ 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/lipg-p-val68 (accessed [today's date]).

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