Is CPLANE1 p.Asn2489fs (c.7466del) pathogenic?

CPLANE1 p.Asn2489fs (c.7466del) is classified Pathogenic in CPLANE1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-30). Absent from gnomAD.

How common is CPLANE1 p.Asn2489fs (c.7466del) in the general population?

CPLANE1 p.Asn2489fs (c.7466del) is absent from gnomAD (gnomAD).

CPLANE1 p.Asn2489fs

c.7466del · rs2150869096 · VCV1453338

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

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 36 of 53
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.1	GERP -2.3, phastCons 0.046

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: CPLANE1
Protein: p.Asn2489fs
Coding: c.7466del
MANE Select: NM_001384732
dbSNP: rs2150869096
Type: Deletion
Location: chr5:37165606 (GRCh38)
Gene constraint: LOEUF 0.728 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 2489: a UniProt-annotated variant site (in ofd6; likely pathogenic)

Full CPLANE1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CPLANE1 p.Asn1182fs Pathogenic ★★ same type
CPLANE1 p.Gln1399fs Pathogenic/Likely pathogenic ★★ same type
CPLANE1 p.Gly2717fs Pathogenic ★★ same type
CPLANE1 p.His961fs Pathogenic/Likely pathogenic ★★ same type
CPLANE1 p.Ile165fs Pathogenic ★★ same type
CPLANE1 p.Ile1889_Asp1890insTer Likely pathogenic ★★ same type
CPLANE1 p.Leu465fs Pathogenic/Likely pathogenic ★★ same type
CPLANE1 p.Leu808fs Pathogenic/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/cplane1-p-asn2489fs (accessed [today's date]).

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