Is LIMA1 p.Phe64Val (c.190T>G) pathogenic?

LIMA1 p.Phe64Val (c.190T>G) is classified Uncertain significance in LIMA1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-14). AlphaMissense: likely benign (0.0904); Absent from gnomAD v4.1.

How common is LIMA1 p.Phe64Val (c.190T>G) in the general population?

LIMA1 p.Phe64Val (c.190T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about LIMA1 p.Phe64Val (c.190T>G)?

AlphaMissense predicts likely benign (score 0.0904) — an in-silico prediction, not a clinical call.

LIMA1 p.Phe64Val

c.190T>G · rs2539966936 · VCV2560212

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0904 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.0904	likely benign
REVEL	0.355	indeterminate
SaProt	LLR -5.40	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 8.1	GERP 1.9, phastCons 1
Regional constraint	o/e 0.86	unconstrained · MANE · 72 kb · p 4.7e-05 · regional, not allelic
Overall
CADD	22.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: LIMA1
Protein: p.Phe64Val
Coding: c.190T>G
MANE Select: NM_016357
dbSNP: rs2539966936
Type: single nucleotide variant
Location: chr12:50222461 (GRCh38)
Gene constraint: LOEUF 1.038 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 52.12 · 1 PDB

Full LIMA1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

LIMA1 p.Ala113Gly Uncertain significance ★ ⚠ same type
LIMA1 p.Ala136Val Uncertain significance ★ ⚠ same type
LIMA1 p.Ala183Asp Uncertain significance ★ ⚠ same type
LIMA1 p.Ala214Ser Uncertain significance ★ ⚠ same type
LIMA1 p.Ala367Val Uncertain significance ★ ⚠ same type
LIMA1 p.Ala479Val Uncertain significance ★ ⚠ same type
LIMA1 p.Ala531Thr Uncertain significance ★ ⚠ same type
LIMA1 p.Arg141Gln 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/lima1-p-phe64val (accessed [today's date]).

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