SEMA4A p.Pro102=
c.306G>A · rs751429275 · VCV2863742
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00439%, 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 -0.34 | GERP -4.5 |
| Overall | ||
| CADD | 9.623 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00439%
South Asian · 4/91,070 alleles
Filtering AF
0.00143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.00062%
10/1,613,952 alleles · very rare
exomes 8/1,461,836 · genomes 2/152,116 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00439% | 22,767 |
| Admixed American | 0.00167% | 59,984 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,484 |
| European (non-Finnish) | 0.000339% | 295,002 |
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
- SEMA4A
- Protein
- p.Pro102=
- Coding
- c.306G>A
- MANE Select
- NM_022367
- dbSNP
- rs751429275
- Type
- single nucleotide variant
- Location
- chr1:156158075 (GRCh38)
- Gene constraint
- LOEUF 0.858 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.05
- Residue 102
- the sema domain
Similar variants
- SEMA4A p.Pro102Arg Uncertain significance ★ ⚠ same residue
- SEMA4A p.Pro102Leu Uncertain significance ★ ⚠ same residue
- SEMA4A p.Pro102Ser Uncertain significance ★ ⚠ same residue
- SEMA4A c.*208A>G Uncertain significance ★★ same type
- SEMA4A p.Ala114Thr Uncertain significance ★★ ⚠ same type
- SEMA4A p.Ala181Thr Uncertain significance ★★ ⚠ same type
- SEMA4A p.Ala337Val Uncertain significance ★★ same type
- SEMA4A p.Ala446Val 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/sema4a-p-pro102 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown