Is CHD2 p.Val1263fs (c.3786_3787del) pathogenic?

CHD2 p.Val1263fs (c.37863787del) is classified Pathogenic in CHD2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-01). Absent from gnomAD.

How common is CHD2 p.Val1263fs (c.3786_3787del) in the general population?

CHD2 p.Val1263fs (c.3786_3787del) is absent from gnomAD (gnomAD).

CHD2 p.Val1263fs

c.3786_3787del · rs869312877 · VCV1335189

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

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; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 30 of 39
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.9	GERP 1.7, 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: CHD2
Protein: p.Val1263fs
Coding: c.3786_3787del
MANE Select: NM_001271
dbSNP: rs869312877
Type: Deletion
Location: chr15:92997300 (GRCh38)
Gene constraint: LOEUF 0.174 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 60.81
Residue 1263: a UniProt-annotated variant site (in dee94); a UniProt-annotated variant site (found in a patient with progressive myoclonus epilepsy; uncertain significance)

Full CHD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CHD2 p.Val1263Leu Uncertain significance ★ ⚠ same residue
CHD2 p.Glu1412fs Pathogenic ★★ same type
CHD2 p.Lys1393fs Pathogenic ★★ same type
CHD2 p.Lys174_Val175insTer Pathogenic/Likely pathogenic ★★ same type
CHD2 p.Pro399fs Pathogenic ★★ same type
CHD2 c.1199-12del Benign/Likely benign ★★ same type
CHD2 c.381+12del Likely benign ★★ same type
CHD2 p.Lys1411del Benign/Likely benign ★★ 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/chd2-p-val1263fs (accessed [today's date]).

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