SP7 p.Ser338=
c.1014G>A · rs756685278 · VCV1427872
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0582%, sas)
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 -14 | GERP -4.1 |
| Overall | ||
| CADD | 0.116 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0582%
South Asian · 53/91,078 alleles
Filtering AF
0.0457%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0412%
Overall
0.0123%
198/1,613,916 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0582% | 1,718 |
| Middle Eastern | 0.0165% | 6,060 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,810 |
| European (non-Finnish) | 0.0103% | 9,671 |
| Finnishnot grpmax-eligible | 0.00938% | 10,660 |
| African / African-American | 0.00666% | 15,010 |
| Admixed American | 0.005% | 20,009 |
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
- SP7
- Protein
- p.Ser338=
- Coding
- c.1014G>A
- MANE Select
- NM_001173467
- dbSNP
- rs756685278
- Type
- single nucleotide variant
- Location
- chr12:53328428 (GRCh38)
- Gene constraint
- LOEUF 0.808 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 52.78
Similar variants
- SP7 p.Ala2Val Uncertain significance ★★ ⚠ same type
- SP7 p.Arg267Cys Uncertain significance ★★ ⚠ same type
- SP7 p.Arg280Leu Uncertain significance ★★ ⚠ same type
- SP7 p.Arg280Trp Uncertain significance ★★ ⚠ same type
- SP7 p.Arg316His Uncertain significance ★★ ⚠ same type
- SP7 p.Arg350Trp Uncertain significance ★★ ⚠ same type
- SP7 p.Arg362His Uncertain significance ★★ ⚠ same type
- SP7 p.Arg365Ter 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/sp7-p-ser338 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown