ARPC5 p.Pro117=
c.351G>A · rs2231240 · VCV1247938
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 20.6%, afr) — too common for a highly-penetrant pathogenic allele
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 -0.66 | GERP -4, phastCons 0.001 |
| Overall | ||
| CADD | 12.34 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
20.6%
African / African-American · 15,436/74,956 alleles
Filtering AF
20.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 20.2%
Overall
3.99%
64,380/1,613,282 alleles · common
exomes 52,347/1,461,062 · genomes 12,033/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 20.6% | 5 |
| South Asian | 6.6% | 15 |
| Middle Eastern | 4.99% | 20 |
| East Asian | 4.91% | 20 |
| Remaining individualsnot grpmax-eligible | 4.47% | 22 |
| European (non-Finnish) | 2.89% | 35 |
| Finnishnot grpmax-eligible | 2.64% | 38 |
| Admixed American | 2.42% | 41 |
| Ashkenazi Jewishnot grpmax-eligible | 1.35% | 74 |
| Amishnot grpmax-eligible | 1.1% | 91 |
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
- ARPC5
- Protein
- p.Pro117=
- Coding
- c.351G>A
- MANE Select
- NM_005717
- dbSNP
- rs2231240
- Type
- single nucleotide variant
- Location
- chr1:183630503 (GRCh38)
- Gene constraint
- LOEUF 0.725 · pLI 0.72 (gnomAD)
- Structure
- AlphaFold pLDDT 92.42 · 2 PDB
- Residue 117
- a UniProt-annotated variant site (in imd113; likely pathogenic; loss of protein expression in patient cells)
Similar variants
- ARPC5 p.Pro117Leu Uncertain significance ★ ⚠ same residue
- ARPC5 p.Ala54Thr Uncertain significance ★ ⚠ same type
- ARPC5 p.Arg47Leu Uncertain significance ★ ⚠ same type
- ARPC5 p.Asn101Ser Uncertain significance ★ ⚠ same type
- ARPC5 p.Asn61Ser Uncertain significance ★ ⚠ same type
- ARPC5 p.Asp104Gly Uncertain significance ★ ⚠ same type
- ARPC5 p.Asp32Glu Uncertain significance ★ ⚠ same type
- ARPC5 p.Ile78Val 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/arpc5-p-pro117 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown