Is SRCAP p.Ser2802= (c.8406C>T) pathogenic?

SRCAP p.Ser2802= (c.8406C>T) is classified Benign/Likely benign in SRCAP (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-01-26). Rare (popmax 0.117%, afr); Associated with Floating-Harbor syndrome.

What condition is associated with SRCAP p.Ser2802= (c.8406C>T)?

SRCAP p.Ser2802= (c.8406C>T) is associated with Floating-Harbor syndrome, developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities (ClinVar).

How common is SRCAP p.Ser2802= (c.8406C>T) in the general population?

SRCAP p.Ser2802= (c.8406C>T) is rare (popmax 0.117%, afr) (gnomAD).

SRCAP p.Ser2802=

c.8406C>T · rs147473528 · VCV1598807

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.117%, afr)

Conditions

Floating-Harbor syndrome

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 0.46	GERP -4.8, phastCons 0.79
Overall
CADD	0.299	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.117% African / African-American · 86/73,200 alleles

Filtering AF 0.0974% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.09%

Overall 0.00757% 118/1,557,806 alleles · rare exomes 72/1,405,512 · genomes 46/152,294 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.117%	851
East Asian	0.0248%	4,039
Remaining individualsnot grpmax-eligible	0.0167%	5,994
South Asian	0.00487%	20,543
Admixed American	0.00194%	51,662
European (non-Finnish)	0.000521%	191,998

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.Ser2802=
Coding: c.8406C>T
MANE Select: NM_006662
dbSNP: rs147473528
Type: single nucleotide variant
Location: chr16:30738446 (GRCh38)
Gene constraint: LOEUF 0.223 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 2802: 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

Also linked: developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities

Similar variants

SRCAP p.Ser2802Phe Conflicting classifications of pathogenicity ★ same residue
SRCAP p.Ser2802Pro Uncertain significance ★ ⚠ same residue
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

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-ser2802 (accessed [today's date]).

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