Is MAP1LC3B p.Arg24Pro (c.71G>C) pathogenic?

MAP1LC3B p.Arg24Pro (c.71G>C) is classified Uncertain significance in MAP1LC3B (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-29). AlphaMissense: likely pathogenic (0.9982); Absent from gnomAD v4.1.

How common is MAP1LC3B p.Arg24Pro (c.71G>C) in the general population?

MAP1LC3B p.Arg24Pro (c.71G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MAP1LC3B p.Arg24Pro (c.71G>C)?

AlphaMissense predicts likely pathogenic (score 0.9982) — an in-silico prediction, not a clinical call.

MAP1LC3B p.Arg24Pro

c.71G>C · VCV4931693

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9982 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.9982	likely pathogenic · top 5% in MAP1LC3B
REVEL	0.525	indeterminate
SaProt	LLR -18.66	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.5	GERP 1.9, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 11 kb · p 0.72 · regional, not allelic
Overall
CADD	28.7	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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: MAP1LC3B
Protein: p.Arg24Pro
Coding: c.71G>C
MANE Select: NM_022818
Type: single nucleotide variant
Location: chr16:87398845 (GRCh38)
Gene constraint: LOEUF 1.24 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.88 · 51 PDB
Residue 24: an α-helix

Full MAP1LC3B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MAP1LC3B p.Arg24= Likely benign ★ same residue
MAP1LC3B p.Asn74Ser Uncertain significance ★ ⚠ same type
MAP1LC3B p.Asn84Lys Uncertain significance ★ ⚠ same type
MAP1LC3B p.Asp56Gly Uncertain significance ★ ⚠ same type
MAP1LC3B p.Gln15Arg Uncertain significance ★ ⚠ same type
MAP1LC3B p.Gln77Arg Uncertain significance ★ ⚠ same type
MAP1LC3B p.Glu102Lys Uncertain significance ★ ⚠ same type
MAP1LC3B p.His86Asp 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/map1lc3b-p-arg24pro (accessed [today's date]).

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