MAP1LC3B p.Arg24=
c.72A>T · rs146238244 · VCV753591
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.144%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.002 | GERP -3.9, phastCons 0.048 |
| Overall | ||
| CADD | 7.59 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.144%
African / African-American · 108/74,932 alleles
Filtering AF
0.122%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.114%
Overall
0.00787%
127/1,614,062 alleles · rare
exomes 57/1,461,834 · genomes 70/152,228 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.144% | 694 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,248 |
| Admixed American | 0.0117% | 8,572 |
| European (non-Finnish) | 0.000169% | 590,005 |
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.Arg24=
- Coding
- c.72A>T
- MANE Select
- NM_022818
- dbSNP
- rs146238244
- Type
- single nucleotide variant
- Location
- chr16:87398846 (GRCh38)
- Gene constraint
- LOEUF 1.24 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.88 · 51 PDB
- Residue 24
- an α-helix
Similar variants
- MAP1LC3B p.Arg24Pro Uncertain significance ★ ⚠ 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-arg24 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown