MAP1LC3B p.Ser115=
c.345C>T · rs1198592237 · VCV749706
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0227%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.12 | GERP -2.7, phastCons 0.97 |
| Overall | ||
| CADD | 7.143 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0227%
African / African-American · 17/74,846 alleles
Filtering AF
0.0144%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0119%
Overall
0.00105%
17/1,612,712 alleles · ultra-rare
exomes 12/1,460,670 · genomes 5/152,042 · joint denominator
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.Ser115=
- Coding
- c.345C>T
- MANE Select
- NM_022818
- dbSNP
- rs1198592237
- Type
- single nucleotide variant
- Location
- chr16:87403064 (GRCh38)
- Gene constraint
- LOEUF 1.24 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.88 · 51 PDB
- Residue 115
- a β-strand
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-ser115 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown