Is DPYD p.Pro712fs (c.2135del) pathogenic?

DPYD p.Pro712fs (c.2135del) is classified Likely pathogenic in DPYD (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-25). Absent from gnomAD.

How common is DPYD p.Pro712fs (c.2135del) in the general population?

DPYD p.Pro712fs (c.2135del) is absent from gnomAD (gnomAD).

DPYD p.Pro712fs

c.2135del · rs1064796552 · VCV423651

Likely pathogenic Single submitter

Classification

Likely 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
NMD	predicted	premature termination codon in exon 17 of 23
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.7	GERP -2.5, 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: DPYD
Protein: p.Pro712fs
Coding: c.2135del
MANE Select: NM_000110
dbSNP: rs1064796552
Type: Deletion
Location: chr1:97306221 (GRCh38)
Gene constraint: LOEUF 1.09 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 96.23

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

Similar variants

DPYD c.1977_1983del Likely pathogenic ★★ same type
DPYD p.Arg589fs Likely pathogenic ★★ same type
DPYD p.Arg916fs Likely pathogenic ★★ same type
DPYD p.Gln860fs Pathogenic/Likely pathogenic ★★ same type
DPYD p.Leu682fs Likely pathogenic ★★ same type
DPYD p.Lys42_Arg43insTer Pathogenic/Likely pathogenic ★★ same type
DPYD c.850+23455_1128+8811del Likely pathogenic ★ same type
DPYD p.Ala946fs Likely pathogenic ★ 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/dpyd-p-pro712fs (accessed [today's date]).

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