SHANK3 p.Ala1007=
c.3021C>A · rs1367333501 · VCV1676468
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,243,464)
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 3.6 | GERP -0.84, phastCons 1 |
| Overall | ||
| CADD | 12.58 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,243,464). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- SHANK3
- Protein
- p.Ala1007=
- Coding
- c.3021C>A
- MANE Select
- NM_001372044
- dbSNP
- rs1367333501
- Type
- single nucleotide variant
- Location
- chr22:50720629 (GRCh38)
- Gene constraint
- LOEUF 0.446 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 53.36 · 3 PDB
- Residue 1007
- the 'disordered' region
Similar variants
- SHANK3 p.Ala1007Thr Uncertain significance ★ same residue
- SHANK3 c.2455+1G>A Pathogenic ★★ same type
- SHANK3 c.2455+1G>C Pathogenic/Likely pathogenic ★★ same type
- SHANK3 c.2838C>G Pathogenic ★★ same type
- SHANK3 p.Arg166Ter Pathogenic/Likely pathogenic ★★ same type
- SHANK3 p.Arg1733Ter Pathogenic/Likely pathogenic ★★ same type
- SHANK3 p.Arg432Ter Pathogenic ★★ same type
- SHANK3 p.Asp1564Tyr Pathogenic ★★ 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/shank3-p-ala1007 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown