ITGAM p.Lys331del
c.989AGA[1] · rs750537448 · VCV1443803
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00288%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 10 | GERP 2.3, phastCons 1 |
| Overall | ||
| CADD | 21.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00288%
European (non-Finnish) · 34/1,179,876 alleles
Filtering AF
0.00207%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00183%
Overall
0.00229%
37/1,613,812 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00288% | 34,702 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,462 |
| Finnishnot grpmax-eligible | 0.00156% | 64,020 |
| African / African-American | 0.00134% | 74,900 |
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
- ITGAM
- Protein
- p.Lys331del
- Coding
- c.989AGA[1]
- MANE Select
- NM_000632
- dbSNP
- rs750537448
- Type
- Microsatellite
- Location
- chr16:31275679 (GRCh38)
- Gene constraint
- LOEUF 0.678 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.30 · 31 PDB
- Residue 331
- an α-helix
Similar variants
- ITGAM c.3388-13_3388-11del Uncertain significance ★ same type
- ITGAM p.Val651fs Uncertain significance ★ same type
- ITGAM c.2364-17TCT[2] Likely benign ★ same type
- ITGAM c.2709-16_2709-15del Likely benign ★ 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/itgam-p-lys331del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown