Is LIPT2 p.Asp24= (c.72C>T) pathogenic?

LIPT2 p.Asp24= (c.72C>T) is classified Likely benign in LIPT2 (ClinVar, Single submitter, 2 submitters; last evaluated 2025-04-09). Ultra-rare (popmax 0.0456%, amr).

How common is LIPT2 p.Asp24= (c.72C>T) in the general population?

LIPT2 p.Asp24= (c.72C>T) is ultra-rare (popmax 0.0456%, amr) (gnomAD).

LIPT2 p.Asp24=

c.72C>T · rs888721791 · VCV2078819

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0456%, amr)

⚠ 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.
REVEL	0.046	moderately benign-leaning
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -1.2	GERP -3
Overall
CADD	13.59	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0456% Admixed American · 18/39,502 alleles

Filtering AF 0.0294% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0243%

Overall 0.00144% 21/1,459,588 alleles · ultra-rare exomes 15/1,307,254 · genomes 6/152,334 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0456%	2,195
South Asian	0.00265%	37,729
Remaining individualsnot grpmax-eligible	0.00178%	56,308

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: LIPT2
Protein: p.Asp24=
Coding: c.72C>T
MANE Select: NM_001144869
dbSNP: rs888721791
Type: single nucleotide variant
Location: chr11:74493632 (GRCh38)

Full LIPT2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/lipt2-p-asp24 (accessed [today's date]).

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