Is SRCAP p.His50fs (c.148del) pathogenic?

SRCAP p.His50fs (c.148del) is classified Pathogenic in SRCAP (ClinVar, Single submitter, 2 submitters; last evaluated 2021-12-10). No gnomAD frequency available for this variant; Associated with neurodevelopmental disorder.

What condition is associated with SRCAP p.His50fs (c.148del)?

SRCAP p.His50fs (c.148del) is associated with neurodevelopmental disorder (ClinVar).

How common is SRCAP p.His50fs (c.148del) in the general population?

SRCAP p.His50fs (c.148del) is no gnomAD frequency available for this variant (gnomAD).

SRCAP p.His50fs

c.148del · rs2052800289 · VCV995439

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

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 4 of 34
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.3	GERP 0.15, phastCons 1

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.His50fs
Coding: c.148del
MANE Select: NM_006662
dbSNP: rs2052800289
Type: Deletion
Location: chr16:30704157 (GRCh38)
Gene constraint: LOEUF 0.223 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 50: 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

Similar variants

SRCAP p.Glu2301fs Pathogenic ★ same condition
SRCAP p.Leu3113fs Likely pathogenic ★ same condition
SRCAP p.Pro278fs Pathogenic ★ same condition
SRCAP p.Gln1519fs Uncertain significance ★ same condition
SRCAP p.Arg2297fs Likely pathogenic same condition
SRCAP p.Gln145fs Likely pathogenic same condition
SRCAP p.Gly598fs Likely pathogenic same condition
SRCAP p.Pro1796fs Likely 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-his50fs (accessed [today's date]).

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