Is SRCAP p.Pro382fs (c.1143_1153delinsTGT) pathogenic?

SRCAP p.Pro382fs (c.11431153delinsTGT) is classified Pathogenic/Likely pathogenic in SRCAP (ClinVar, No assertion criteria, 2 submitters; last evaluated 2021-11-08). No gnomAD frequency available for this variant; Associated with neurodevelopmental disorder.

What condition is associated with SRCAP p.Pro382fs (c.1143_1153delinsTGT)?

SRCAP p.Pro382fs (c.1143_1153delinsTGT) is associated with neurodevelopmental disorder, developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities (ClinVar).

How common is SRCAP p.Pro382fs (c.1143_1153delinsTGT) in the general population?

SRCAP p.Pro382fs (c.1143_1153delinsTGT) is no gnomAD frequency available for this variant (gnomAD).

SRCAP p.Pro382fs

c.1143_1153delinsTGT · rs2151287951 · VCV995422

Pathogenic/Likely pathogenic No assertion criteria

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

neurodevelopmental disorder

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	predicted	premature termination codon in exon 9 of 34
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.95	GERP -5.2

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.Pro382fs
Coding: c.1143_1153delinsTGT
MANE Select: NM_006662
dbSNP: rs2151287951
Type: Indel
Location: chr16:30710762 (GRCh38)
Gene constraint: LOEUF 0.223 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 382: the 'disordered' region

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

Disease context

neurodevelopmental disorder — 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.Ala1721Leu Uncertain significance ★★ same condition
SRCAP p.Arg389Leu Uncertain significance ★ same condition
SRCAP p.Ser1821fs Uncertain significance ★ same condition
SRCAP p.Gln537fs Likely pathogenic same condition
SRCAP p.Arg2444Ter Pathogenic ★★ same condition
SRCAP p.Arg2718Ter Pathogenic/Likely pathogenic ★★ same condition
SRCAP p.Pro1879fs Pathogenic/Likely pathogenic ★★ same condition
SRCAP c.2130+6A>T 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-pro382fs (accessed [today's date]).

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