ACP5 p.Val253=
c.759G>A · rs1973087424 · VCV2975663
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Conditions
1
Spondyloenchondrodysplasia with immune dysregulation
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 -0.16 | GERP -2.9, phastCons 0.27 |
| Overall | ||
| CADD | 0.875 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,024 alleles
Overall
0.000657%
1/152,114 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
- ACP5
- Protein
- p.Val253=
- Coding
- c.759G>A
- MANE Select
- NM_001611
- dbSNP
- rs1973087424
- Type
- single nucleotide variant
- Location
- chr19:11575229 (GRCh38)
- Gene constraint
- LOEUF 1.14 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 94.82 · 2 PDB
Similar variants
- ACP5 p.Val253Ala Uncertain significance ★ ⚠ same residue
- ACP5 p.Val253Met Uncertain significance ★ ⚠ same residue
- ACP5 p.Arg176Ter Pathogenic ★★ same condition
- ACP5 p.Gln184Ter Pathogenic/Likely pathogenic ★★ same condition
- ACP5 p.Gly109Arg Pathogenic/Likely pathogenic ★★ same condition
- ACP5 p.Met264Lys Pathogenic/Likely pathogenic ★★ ⚠ same condition
- ACP5 p.Tyr123Ter Pathogenic ★★ same condition
- ACP5 p.Tyr246Ter Pathogenic/Likely pathogenic ★★ same condition
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/acp5-p-val253 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown