Is DPYD p.Cys257= (c.771C>T) pathogenic?

DPYD p.Cys257= (c.771C>T) is classified Likely benign in DPYD (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-10). Ultra-rare (popmax 0.0408%, eas); Associated with Inborn genetic diseases.

What condition is associated with DPYD p.Cys257= (c.771C>T)?

DPYD p.Cys257= (c.771C>T) is associated with Inborn genetic diseases (ClinVar).

How common is DPYD p.Cys257= (c.771C>T) in the general population?

DPYD p.Cys257= (c.771C>T) is ultra-rare (popmax 0.0408%, eas) (gnomAD).

DPYD p.Cys257=

c.771C>T · rs754745863 · VCV3230333

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0408%, eas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1	GERP -4.1, phastCons 0.99
Overall
CADD	5.127	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0408% East Asian · 18/44,092 alleles

Filtering AF 0.0263% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0217%

Overall 0.00528% 82/1,553,110 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0408%	2,450
Middle Eastern	0.0196%	5,108
Admixed American	0.00865%	11,561
Remaining individualsnot grpmax-eligible	0.00833%	12,002
South Asian	0.00713%	14,031
European (non-Finnish)	0.00396%	25,269
African / African-American	0.00271%	36,852

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: DPYD
Protein: p.Cys257=
Coding: c.771C>T
MANE Select: NM_000110
dbSNP: rs754745863
Type: single nucleotide variant
Location: chr1:97679174 (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

Disease context

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

Similar variants

DPYD p.Cys257Tyr Uncertain significance ★ ⚠ same residue
DPYD p.Cys257Ter Likely pathogenic ★ same residue
DPYD p.Ala513Val Uncertain significance ★★ ⚠ same condition
DPYD p.Ala664Ser Uncertain significance ★★ ⚠ same condition
DPYD p.Arg332Gln Uncertain significance ★★ ⚠ same condition
DPYD p.Arg410Gln Uncertain significance ★★ ⚠ same condition
DPYD p.Arg692Gln Uncertain significance ★★ ⚠ same condition
DPYD p.Gln508= 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/dpyd-p-cys257 (accessed [today's date]).

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