ITGAM p.Cys73=
c.219C>T · rs200003591 · VCV1437382
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0429%, 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 -2.7 | GERP -4.2 |
| Overall | ||
| CADD | 8.353 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0429%
African / African-American · 32/74,606 alleles
Filtering AF
0.0311%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0272%
Overall
0.00982%
157/1,599,474 alleles · ultra-rare
exomes 123/1,447,210 · genomes 34/152,264 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0429% | 2,331 |
| Admixed American | 0.0242% | 4,129 |
| European (non-Finnish) | 0.00895% | 11,172 |
| Remaining individualsnot grpmax-eligible | 0.00808% | 12,377 |
| East Asian | 0.00226% | 44,214 |
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.Cys73=
- Coding
- c.219C>T
- MANE Select
- NM_000632
- dbSNP
- rs200003591
- Type
- single nucleotide variant
- Location
- chr16:31265479 (GRCh38)
- Gene constraint
- LOEUF 0.678 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.30 · 31 PDB
- Residue 73
- a disulfide bond; a β-strand
Similar variants
- ITGAM p.Cys73Gly Uncertain significance ★ ⚠ same residue
- ITGAM c.704+5G>A Uncertain significance ★★ same type
- ITGAM p.Ala31Thr Uncertain significance ★★ ⚠ same type
- ITGAM p.Ala433Val Uncertain significance ★★ ⚠ same type
- ITGAM p.Ala753Val Uncertain significance ★★ ⚠ same type
- ITGAM p.Ala943Val Uncertain significance ★★ ⚠ same type
- ITGAM p.Arg1003His Uncertain significance ★★ ⚠ same type
- ITGAM p.Arg131Trp 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/itgam-p-cys73 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown