ARPC2 p.Leu3=
c.7C>T · rs144937426 · VCV781689
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.45%, amr)
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 3.9 | GERP -0.069, phastCons 1 |
| Overall | ||
| CADD | 14.77 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.45%
Admixed American · 2,070/60,012 alleles
Filtering AF
3.33%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.28%
Overall
0.642%
10,354/1,613,918 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 3.45% | 29 |
| East Asian | 2.13% | 47 |
| Remaining individualsnot grpmax-eligible | 0.606% | 165 |
| European (non-Finnish) | 0.546% | 183 |
| Finnishnot grpmax-eligible | 0.386% | 259 |
| African / African-American | 0.168% | 596 |
| Middle Eastern | 0.165% | 606 |
| South Asian | 0.113% | 884 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0574% | 1,741 |
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
- ARPC2
- Protein
- p.Leu3=
- Coding
- c.7C>T
- MANE Select
- NM_152862
- dbSNP
- rs144937426
- Type
- single nucleotide variant
- Location
- chr2:218217477 (GRCh38)
- Gene constraint
- LOEUF 0.319 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 94.03 · 5 PDB
Similar variants
- ARPC2 c.677-3C>T Benign ★★ same type
- ARPC2 p.Ala69Val Uncertain significance ★ ⚠ same type
- ARPC2 p.Arg237Gln Uncertain significance ★ ⚠ same type
- ARPC2 p.Arg267Trp Uncertain significance ★ ⚠ same type
- ARPC2 p.Arg281Cys Uncertain significance ★ ⚠ same type
- ARPC2 p.Arg281His Uncertain significance ★ ⚠ same type
- ARPC2 p.Arg300His Uncertain significance ★ ⚠ same type
- ARPC2 p.Asn219Asp 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/arpc2-p-leu3 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown