Is MAP1LC3B p.Val91Ile (c.271G>A) pathogenic?

MAP1LC3B p.Val91Ile (c.271G>A) is classified Uncertain significance in MAP1LC3B (ClinVar, Single submitter, 1 submitter; last evaluated 2021-06-22). AlphaMissense: likely benign (0.1926); Very rare (popmax 0.00907%, nfe).

How common is MAP1LC3B p.Val91Ile (c.271G>A) in the general population?

MAP1LC3B p.Val91Ile (c.271G>A) is very rare (popmax 0.00907%, nfe) (gnomAD).

What do computational predictors say about MAP1LC3B p.Val91Ile (c.271G>A)?

AlphaMissense predicts likely benign (score 0.1926) — an in-silico prediction, not a clinical call.

MAP1LC3B p.Val91Ile

c.271G>A · rs149003518 · VCV2406999

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1926 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00907%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1926	likely benign
REVEL	0.172	moderately benign-leaning
SaProt	LLR -11.89	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.5	GERP 1.1, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 11 kb · p 0.72 · regional, not allelic
Overall
CADD	24.6	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00907% European (non-Finnish) · 107/1,179,920 alleles

Filtering AF 0.00766% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00708%

Overall 0.00731% 118/1,613,922 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00907%	11,027
Remaining individualsnot grpmax-eligible	0.0064%	15,617
African / African-American	0.004%	24,973
South Asian	0.00329%	30,362
Finnishnot grpmax-eligible	0.00156%	64,038

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: MAP1LC3B
Protein: p.Val91Ile
Coding: c.271G>A
MANE Select: NM_022818
dbSNP: rs149003518
Type: single nucleotide variant
Location: chr16:87402990 (GRCh38)
Gene constraint: LOEUF 1.24 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.88 · 51 PDB
Residue 91: a turn

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

Similar variants

MAP1LC3B p.Arg24Pro Uncertain significance ★ ⚠ same type
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-val91ile (accessed [today's date]).

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