Is DPF2 p.Cys276Phe (c.827G>T) pathogenic?

DPF2 p.Cys276Phe (c.827G>T) is classified Pathogenic in DPF2 (ClinVar, Single submitter, 2 submitters; last evaluated 2017-09-14). AlphaMissense: likely pathogenic (0.9999); Absent from gnomAD v4.1; Associated with Coffin-Siris syndrome 1.

What condition is associated with DPF2 p.Cys276Phe (c.827G>T)?

DPF2 p.Cys276Phe (c.827G>T) is associated with Coffin-Siris syndrome 1, Coffin-Siris syndrome 7 (ClinVar).

How common is DPF2 p.Cys276Phe (c.827G>T) in the general population?

DPF2 p.Cys276Phe (c.827G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DPF2 p.Cys276Phe (c.827G>T)?

AlphaMissense predicts likely pathogenic (score 0.9999) — an in-silico prediction, not a clinical call.

DPF2 p.Cys276Phe

c.827G>T · rs1555031372 · VCV438643

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.9999 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Coffin-Siris syndrome 1

Computational evidence

Protein change
AlphaMissense	0.9999	likely pathogenic ✓ concordant with ClinVar · top 9% in DPF2
REVEL	0.923	moderately pathogenic-leaning
SaProt	LLR -14.53	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.9, phastCons 1
Regional constraint	o/e 0.69	unconstrained · MANE · 341 bp · p 0.0039 · regional, not allelic
Overall
CADD	28.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: DPF2
Protein: p.Cys276Phe
Coding: c.827G>T
MANE Select: NM_006268
dbSNP: rs1555031372
Type: single nucleotide variant
Location: chr11:65345981 (GRCh38)
Gene constraint: LOEUF 0.287 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 69.62 · 9 PDB
Residue 276: a UniProt-annotated variant site (in css7; abolishes interaction with acetylated or methylated histone h3); a turn

Full DPF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Coffin-Siris syndrome 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Coffin-Siris syndrome 7

Similar variants

DPF2 p.Arg350His Pathogenic/Likely pathogenic ★★ same condition
DPF2 p.Asp346Asn Likely pathogenic ★★ same condition
DPF2 p.Ala133Pro Uncertain significance ★★ ⚠ same condition
DPF2 c.302-11C>T Likely benign ★★ same condition
DPF2 c.904+1G>T Pathogenic ★ same condition
DPF2 p.Arg300Leu Likely pathogenic ★ same condition
DPF2 p.Asp346Gly Pathogenic ★ same condition
DPF2 p.Cys324Gly 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/dpf2-p-cys276phe (accessed [today's date]).

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