SRCAP p.Ser3148=
c.9444T>C · rs142948420 · VCV196909
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Rare
rare (popmax 0.749%, afr)
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 -0.021 | GERP -3.2, phastCons 0.073 |
| Overall | ||
| CADD | 3.801 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.749%
African / African-American · 562/74,994 alleles
Filtering AF
0.698%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.678%
Overall
0.0384%
619/1,613,768 alleles · rare
exomes 312/1,461,600 · genomes 307/152,168 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.749% | 133 |
| Admixed American | 0.04% | 2,500 |
| Remaining individualsnot grpmax-eligible | 0.0368% | 2,717 |
| Middle Eastern | 0.033% | 3,030 |
| South Asian | 0.0022% | 45,540 |
| European (non-Finnish) | 0.000509% | 196,656 |
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.Ser3148=
- Coding
- c.9444T>C
- MANE Select
- NM_006662
- dbSNP
- rs142948420
- Type
- single nucleotide variant
- Location
- chr16:30739484 (GRCh38)
- Gene constraint
- LOEUF 0.223 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 3148
- the 'disordered' region; a UniProt-annotated variant site (in dehmba); a UniProt-annotated variant site (in flhs)
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-ser3148 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown