Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Common
common (popmax 100%, eas) — too common for a highly-penetrant pathogenic allele
Conditions
2
developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities
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 0.53 | GERP -3.6, phastCons 0.93 |
| Overall | ||
| CADD | 0.702 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
100%
East Asian · 44,808/44,808 alleles
Filtering AF
99.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 99.8%
Overall
99.6%
1,607,146/1,612,930 alleles · common
exomes 1,459,056/1,461,874 · genomes 148,090/151,056 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 100% | 1 |
| Finnishnot grpmax-eligible | 100% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 100% | 1 |
| Amishnot grpmax-eligible | 100% | 1 |
| European (non-Finnish) | 100% | 1 |
| South Asian | 100% | 1 |
| Middle Eastern | 99.9% | 1 |
| Admixed American | 99.7% | 1 |
| Remaining individualsnot grpmax-eligible | 99.6% | 1 |
| African / African-American | 92.9% | 1 |
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
- SRCAP
- Protein
- p.Ser1406=
- Coding
- c.4218C>A
- MANE Select
- NM_006662
- dbSNP
- rs4889502
- Type
- single nucleotide variant
- Location
- chr16:30723642 (GRCh38)
- Gene constraint
- LOEUF 0.223 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 1406
- the 'disordered' region; a UniProt-annotated variant site (in dehmba)
Similar variants
- SRCAP p.Arg2329Ter Pathogenic/Likely pathogenic ★★ same condition
- SRCAP p.Arg2435Ter Pathogenic/Likely pathogenic ★★ same condition
- SRCAP p.Arg2444Ter Pathogenic ★★ same condition
- SRCAP p.Arg2718Ter Pathogenic/Likely pathogenic ★★ same condition
- SRCAP p.Arg2748Ter Pathogenic ★★ same condition
- SRCAP p.Gln2407Ter Pathogenic ★★ same condition
- SRCAP p.Gln2419Ter Pathogenic ★★ same condition
- SRCAP p.Gln2665Ter Pathogenic/Likely pathogenic ★★ same condition
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/srcap-p-ser1406 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown