SND1 p.Pro43=
c.129T>A · rs567874929 · VCV744005
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0131%, 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 -0.19 | GERP -1.9, phastCons 0.69 |
| Overall | ||
| CADD | 11.58 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0131%
European (non-Finnish) · 154/1,180,022 alleles
Filtering AF
0.0113%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0107%
Overall
0.00991%
160/1,614,018 alleles · ultra-rare
exomes 150/1,461,866 · genomes 10/152,152 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0131% | 7,662 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,621 |
| Admixed American | 0.00333% | 29,999 |
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
- SND1
- Protein
- p.Pro43=
- Coding
- c.129T>A
- MANE Select
- NM_014390
- dbSNP
- rs567874929
- Type
- single nucleotide variant
- Location
- chr7:127686663 (GRCh38)
- Gene constraint
- LOEUF 0.386 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 90.24 · 11 PDB
- Residue 43
- the tnase-like 1 domain; a β-strand
Similar variants
- SND1 p.Lys491Arg Uncertain significance ★★ ⚠ same type
- SND1 p.Ala5= Likely benign ★★ same type
- SND1 p.Gln516= Benign ★★ same type
- SND1 p.Gly307= Benign ★★ same type
- LRRC4 p.His299Asp Uncertain significance ★ ⚠ same type
- SND1 p.Ala15Gly Uncertain significance ★ ⚠ same type
- SND1 p.Ala308Thr Uncertain significance ★ ⚠ same type
- SND1 p.Ala514Thr 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/snd1-p-pro43 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown