Is CPS1 p.Lys219fs (c.656_657del) pathogenic?

CPS1 p.Lys219fs (c.656657del) is classified Likely pathogenic in CPS1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-16). Absent from gnomAD; Associated with pulmonary hypertension, neonatal, susceptibility to.

What condition is associated with CPS1 p.Lys219fs (c.656_657del)?

CPS1 p.Lys219fs (c.656_657del) is associated with pulmonary hypertension, neonatal, susceptibility to (ClinVar).

How common is CPS1 p.Lys219fs (c.656_657del) in the general population?

CPS1 p.Lys219fs (c.656_657del) is absent from gnomAD (gnomAD).

CPS1 p.Lys219fs

c.656_657del · rs2469112567 · VCV3241194

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

Conditions

pulmonary hypertension, neonatal, susceptibility to

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 7 of 38
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.4	GERP 1.2, phastCons 0.01

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: CPS1
Protein: p.Lys219fs
Coding: c.656_657del
MANE Select: NM_001875
dbSNP: rs2469112567
Type: Deletion
Location: chr2:210588090 (GRCh38)
Gene constraint: LOEUF 0.764 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.80 · 14 PDB
Residue 219: the glutamine amidotransferase type-1 domain; a β-strand; a modified residue (n6-acetyllysine; alternate); a modified residue (n6-glutaryllysine; alternate)

Full CPS1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

pulmonary hypertension, neonatal, susceptibility to — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CPS1 p.Ala907fs Pathogenic/Likely pathogenic ★★ same condition
CPS1 p.Arg1228fs Pathogenic/Likely pathogenic ★★ same condition
CPS1 p.Arg932_Leu933insTer Pathogenic ★★ same condition
CPS1 p.Asp642fs Pathogenic/Likely pathogenic ★★ same condition
CPS1 p.Glu842fs Pathogenic/Likely pathogenic ★★ same condition
CPS1 p.Gly475fs Pathogenic/Likely pathogenic ★★ same condition
CPS1 p.Gly510fs Pathogenic ★★ same condition
CPS1 p.His974fs Pathogenic/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/cps1-p-lys219fs (accessed [today's date]).

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