Is DPH1 p.Pro169fs (c.501del) pathogenic?

DPH1 p.Pro169fs (c.501del) is classified Likely pathogenic in DPH1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-06). Associated with developmental delay with short stature, dysmorphic facial features, and sparse hair 1.

DPH1 p.Pro169fs

Q: What condition is associated with DPH1 p.Pro169fs (c.501del)?

DPH1 p.Pro169fs (c.501del) is associated with developmental delay with short stature, dysmorphic facial features, and sparse hair 1 (ClinVar).

c.501del · VCV4854548

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

developmental delay with short stature, dysmorphic facial features, and sparse hair 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 5 of 13
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.4	GERP 1.3, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: DPH1
Protein: p.Pro169fs
Coding: c.501del
MANE Select: NM_001383
Type: Deletion
Location: chr17:2036627 (GRCh38)
Gene constraint: LOEUF 1.321 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.00

Full DPH1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

developmental delay with short stature, dysmorphic facial features, and sparse hair 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DPH1 p.Glu92fs Pathogenic/Likely pathogenic ★★ same condition
DPH1 p.Tyr263del Uncertain significance ★★ same condition
DPH1 p.Pro169Leu Uncertain significance ★ ⚠ same residue
DPH1 p.Leu229Pro Pathogenic/Likely pathogenic ★★ same condition
DPH1 p.Arg144Trp Uncertain significance ★★ ⚠ same condition
DPH1 p.Arg22Gln Uncertain significance ★★ ⚠ same condition
DPH1 p.Arg47Trp Uncertain significance ★★ ⚠ same condition
DPH1 p.Asp231Glu 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/dph1-p-pro169fs (accessed [today's date]).

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