Is SRCAP p.Ser2489del (c.7464_7466del) pathogenic?

SRCAP p.Ser2489del (c.74647466del) is classified Uncertain significance in SRCAP (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-15). Associated with developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities.

SRCAP p.Ser2489del

Q: What condition is associated with SRCAP p.Ser2489del (c.7464_7466del)?

SRCAP p.Ser2489del (c.7464_7466del) is associated with developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities, Floating-Harbor syndrome (ClinVar).

c.7464_7466del · VCV3580214

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

Conditions

developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities

Computational evidence

Protein change
Missense predictors do not apply to this variant type.
Splicing
SpliceAI	—	not assessed · substitutions only
Region caveats
Repeat context	tandem	(CCT)n simple repeat · ambiguous alignment · confidence, not pathogenicity

Variant & gene context

Gene: SRCAP
Protein: p.Ser2489del
Coding: c.7464_7466del
MANE Select: NM_006662
Type: Deletion
Location: chr16:30737503 (GRCh38)
Gene constraint: LOEUF 0.223 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 2489: a UniProt-annotated variant site (in dehmba); a UniProt-annotated variant site (in flhs)

Full SRCAP gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Floating-Harbor syndrome

Similar variants

SRCAP p.Pro2459fs Pathogenic/Likely pathogenic ★★ same condition
SRCAP p.Pro2461fs Pathogenic ★★ same condition
SRCAP p.Val1012del Uncertain significance ★★ same condition
SRCAP c.1187_1228+67del Likely pathogenic ★ same condition
SRCAP c.1319del Pathogenic ★ same condition
SRCAP c.2298_2300+3del Pathogenic ★ same condition
SRCAP p.Ala2262fs Pathogenic ★ same condition
SRCAP p.Arg1897fs 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-ser2489del (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown