Is LIPT2 p.Arg29= (c.87G>T) pathogenic?

LIPT2 p.Arg29= (c.87G>T) is classified Likely benign in LIPT2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-12). No allele count reported in gnomAD v4.1 (AN 1,457,778).

How common is LIPT2 p.Arg29= (c.87G>T) in the general population?

LIPT2 p.Arg29= (c.87G>T) is no allele count reported in gnomAD v4.1 (AN 1,457,778) (gnomAD).

LIPT2 p.Arg29=

c.87G>T · rs2496154767 · VCV2134808

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,457,778)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.014	strongly benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.13	GERP -1.8, phastCons 0.5
Overall
CADD	13.66	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,457,778). 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: LIPT2
Protein: p.Arg29=
Coding: c.87G>T
MANE Select: NM_001144869
dbSNP: rs2496154767
Type: single nucleotide variant
Location: chr11:74493617 (GRCh38)
Gene constraint: LOEUF 1.954 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.37

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

Similar variants

LIPT2 p.Ala121Val Uncertain significance ★★ ⚠ same type
LIPT2 p.Ala75Thr Uncertain significance ★★ ⚠ same type
LIPT2 p.Arg158Cys Uncertain significance ★★ ⚠ same type
LIPT2 p.Arg2Gln Uncertain significance ★★ ⚠ same type
LIPT2 p.Asp134Ala Uncertain significance ★★ ⚠ same type
LIPT2 p.Gln133Glu Uncertain significance ★★ ⚠ same type
LIPT2 p.Glu207Lys Uncertain significance ★★ ⚠ same type
LIPT2 p.Gly109Asp 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/lipt2-p-arg29 (accessed [today's date]).

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