Is PRUNE1 p.Asp3fs (c.3_7dup) pathogenic?

PRUNE1 p.Asp3fs (c.37dup) is classified Pathogenic in PRUNE1 (ClinVar, Single submitter, 1 submitter; last evaluated 2017-05-16). Absent from gnomAD; Associated with Inborn genetic diseases.

What condition is associated with PRUNE1 p.Asp3fs (c.3_7dup)?

PRUNE1 p.Asp3fs (c.3_7dup) is associated with Inborn genetic diseases (ClinVar).

How common is PRUNE1 p.Asp3fs (c.3_7dup) in the general population?

PRUNE1 p.Asp3fs (c.3_7dup) is absent from gnomAD (gnomAD).

PRUNE1 p.Asp3fs

c.3_7dup · rs1553251507 · VCV521739

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

Conditions

Inborn genetic diseases

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 1 of 8
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	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: PRUNE1
Protein: p.Asp3fs
Coding: c.3_7dup
MANE Select: NM_021222
dbSNP: rs1553251507
Type: Duplication
Location: chr1:151008634 (GRCh38)
Gene constraint: LOEUF 0.902 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.61

Full PRUNE1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PRUNE1 p.Asp87Asn Uncertain significance ★★ ⚠ same condition
PRUNE1 p.Ser391Asn Uncertain significance ★★ ⚠ same condition
PRUNE1 p.Thr311Met Uncertain significance ★★ ⚠ same condition
PRUNE1 p.Ala221fs Pathogenic ★ same condition
PRUNE1 p.Asp364Val Uncertain significance ★ ⚠ same condition
PRUNE1 p.Glu435Lys Uncertain significance ★ ⚠ same condition
PRUNE1 p.Ser321Phe Uncertain significance ★ ⚠ same condition
PRUNE1 p.Ser370Ter 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/prune1-p-asp3fs (accessed [today's date]).

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