Is SRCAP p.Ser2463fs (c.7387del) pathogenic?

SRCAP p.Ser2463fs (c.7387del) is classified Pathogenic in SRCAP (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-08-16). No gnomAD frequency available for this variant.

How common is SRCAP p.Ser2463fs (c.7387del) in the general population?

SRCAP p.Ser2463fs (c.7387del) is no gnomAD frequency available for this variant (gnomAD).

SRCAP p.Ser2463fs

c.7387del · rs2506727189 · VCV2024360

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type.
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
Region caveats
Repeat context	tandem	(CCAGCT)n simple repeat · ambiguous alignment · confidence, not pathogenicity

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.Ser2463fs
Coding: c.7387del
MANE Select: NM_006662
dbSNP: rs2506727189
Type: Deletion
Location: chr16:30737425 (GRCh38)
Gene constraint: LOEUF 0.223 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 2463: 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

Similar variants

SRCAP p.Pro2459fs Pathogenic/Likely pathogenic ★★ same type
SRCAP p.Pro2461fs Pathogenic ★★ same type
SRCAP p.Thr572del Uncertain significance ★★ same type
SRCAP p.Val1012del Uncertain significance ★★ same type
SRCAP p.Phe1867del Benign/Likely benign ★★ same type
SRCAP c.1187_1228+67del Likely pathogenic ★ same type
SRCAP c.1319del Pathogenic ★ same type
SRCAP c.2298_2300+3del Pathogenic ★ same type

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-ser2463fs (accessed [today's date]).

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