Is SRCAP c.1319del pathogenic?

SRCAP c.1319del is classified Pathogenic in SRCAP (ClinVar, Single submitter, 1 submitter). No gnomAD frequency available for this variant; Associated with developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities.

How common is SRCAP c.1319del in the general population?

SRCAP c.1319del is no gnomAD frequency available for this variant (gnomAD).

SRCAP c.1319del

Q: What condition is associated with SRCAP c.1319del?

SRCAP c.1319del is associated with developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities, Floating-Harbor syndrome (ClinVar).

rs2506627905 · VCV3024229

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

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 · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 2.5, phastCons 1
Non-coding constraint	Z 0.17	1 kb window · o/e 0.99 · regional · uncalibrated

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: SRCAP
Coding: c.1319del
MANE Select: NM_006662
dbSNP: rs2506627905
Type: Deletion
Location: chr16:30711570 (GRCh38)
Gene constraint: LOEUF 0.223 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)

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.2298_2300+3del Pathogenic ★ same condition
SRCAP p.Ala2262fs Pathogenic ★ same condition
SRCAP p.Arg1897fs Pathogenic ★ same condition
SRCAP p.Gln2517fs 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-c-1319del (accessed [today's date]).

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