CARMIL2 p.Pro1003=
c.3009G>T · VCV4780026
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000328%, nfe)
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 -0.96 | GERP -2.2 |
| Overall | ||
| CADD | 3.076 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000328%
European (non-Finnish) · 3/913,992 alleles
Filtering AF
8.7e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.4e-05%
Overall
0.00031%
3/968,000 alleles · very rare
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
- CARMIL2
- Protein
- p.Pro1003=
- Coding
- c.3009G>T
- MANE Select
- NM_001013838
- Type
- single nucleotide variant
- Location
- chr16:67653143 (GRCh38)
- Gene constraint
- LOEUF 0.701 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.50
- Residue 1003
- the 'disordered' region; a UniProt-annotated variant site (in imd58; no detectable protein expression in patient's leukocytes; no effect on homodimerization)
Similar variants
- CARMIL2 c.1334+1G>T Likely pathogenic ★★ same type
- CARMIL2 c.2313+1G>A Likely pathogenic ★★ same type
- CARMIL2 c.871+1G>T Pathogenic ★★ same type
- CARMIL2 c.958+1G>A Likely pathogenic ★★ same type
- CARMIL2 p.Arg174Ter Pathogenic/Likely pathogenic ★★ same type
- CARMIL2 p.Asn530Lys Pathogenic/Likely pathogenic ★★ same type
- CARMIL2 p.Gln1379Ter Pathogenic/Likely pathogenic ★★ same type
- CARMIL2 p.Ser370Ter Pathogenic ★★ 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/carmil2-p-pro1003 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown