Is SRCAP p.Val2646fs (c.7937_7938del) pathogenic?

SRCAP p.Val2646fs (c.79377938del) is classified Likely pathogenic in SRCAP (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-29). No gnomAD frequency available for this variant; Associated with Floating-Harbor syndrome.

What condition is associated with SRCAP p.Val2646fs (c.7937_7938del)?

SRCAP p.Val2646fs (c.7937_7938del) is associated with Floating-Harbor syndrome (ClinVar).

How common is SRCAP p.Val2646fs (c.7937_7938del) in the general population?

SRCAP p.Val2646fs (c.7937_7938del) is no gnomAD frequency available for this variant (gnomAD).

SRCAP p.Val2646fs

c.7937_7938del · rs2506729448 · VCV1802599

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Floating-Harbor syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	escapes	premature termination codon in the last exon (34 of 34) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -3.2	GERP -4.5

Predicted loss-of-function is descriptive, not an applied PVS1 code.

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
Protein: p.Val2646fs
Coding: c.7937_7938del
MANE Select: NM_006662
dbSNP: rs2506729448
Type: Microsatellite
Location: chr16:30737971 (GRCh38)
Gene constraint: LOEUF 0.223 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 2646: the 'disordered' region; 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

Floating-Harbor syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SRCAP p.Gln2770del Uncertain significance ★★ same condition
SRCAP p.Glu3182del Uncertain significance ★★ same condition
SRCAP p.Pro2488del Uncertain significance ★★ same condition
SRCAP p.Ser2576del Uncertain significance ★★ same condition
SRCAP p.Val2646Met Uncertain significance ★★ ⚠ same residue
SRCAP p.Glu2405fs Pathogenic ★ same condition
SRCAP p.Arg2768_Gln2769insArg Uncertain significance ★ same condition
SRCAP p.Asp548del Uncertain significance ★ 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-val2646fs (accessed [today's date]).

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