SRP72 p.Pro507=
c.1521A>G · rs936610987 · VCV1621964
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.015%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.24 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.056 | GERP -1.1, phastCons 0.56 |
| Overall | ||
| CADD | 8.392 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.015%
Admixed American · 9/59,990 alleles
Filtering AF
0.00773%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00579%
Overall
0.000868%
14/1,613,746 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.015% | 6,666 |
| African / African-American | 0.00133% | 74,916 |
| European (non-Finnish) | 0.000339% | 294,976 |
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
- SRP72
- Protein
- p.Pro507=
- Coding
- c.1521A>G
- MANE Select
- NM_006947
- dbSNP
- rs936610987
- Type
- single nucleotide variant
- Location
- chr4:56491449 (GRCh38)
- Gene constraint
- LOEUF 0.58 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 82.76 · 7 PDB
- Residue 507
- the 'required for the interaction with the srp68/7sl rna complex' region
Similar variants
- SRP72 p.Pro507Ala Uncertain significance ★ ⚠ same residue
- SRP72 c.1502+1G>A Uncertain significance ★★ same type
- SRP72 c.1640+4A>G Uncertain significance ★★ same type
- SRP72 c.768-9T>G Uncertain significance ★★ same type
- SRP72 p.Ala13Thr Uncertain significance ★★ ⚠ same type
- SRP72 p.Ala156Gly Uncertain significance ★★ ⚠ same type
- SRP72 p.Ala185Val Uncertain significance ★★ ⚠ same type
- SRP72 p.Ala291Val 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/srp72-p-pro507 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown