Is CPLANE1 p.Val2891fs (c.8672_8678delinsAT) pathogenic?

CPLANE1 p.Val2891fs (c.86728678delinsAT) is classified Pathogenic in CPLANE1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-04). Absent from gnomAD.

How common is CPLANE1 p.Val2891fs (c.8672_8678delinsAT) in the general population?

CPLANE1 p.Val2891fs (c.8672_8678delinsAT) is absent from gnomAD (gnomAD).

CPLANE1 p.Val2891fs

c.8672_8678delinsAT · rs1064796131 · VCV422968

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 46 of 53
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5.6	GERP -0.28, 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: CPLANE1
Protein: p.Val2891fs
Coding: c.8672_8678delinsAT
MANE Select: NM_001384732
dbSNP: rs1064796131
Type: Indel
Location: chr5:37138834 (GRCh38)
Gene constraint: LOEUF 0.728 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 2891: 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.Ala2276Pro Uncertain significance ★★ same type
CPLANE1 p.Glu2776Phe Uncertain significance ★★ same type
CPLANE1 p.Leu463Pro Uncertain significance ★★ same type
CPLANE1 p.Gly834fs Likely pathogenic ★ same type
CPLANE1 p.Pro1236fs Likely pathogenic ★ same type
CPLANE1 p.Ser724fs Likely pathogenic ★ same type
CPLANE1 p.Trp2261_Gly2262delinsTer Likely pathogenic ★ same type
CPLANE1 c.5421+5_5421+11delinsTGATAAATACAATTGATA Uncertain significance ★ 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-val2891fs (accessed [today's date]).

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