Is CPLANE1 p.Ser2719fs (c.8155_8156del) pathogenic?

CPLANE1 p.Ser2719fs (c.81558156del) is classified Likely pathogenic in CPLANE1 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-10-16). Absent from gnomAD; Associated with Median cleft lip and palate.

What condition is associated with CPLANE1 p.Ser2719fs (c.8155_8156del)?

CPLANE1 p.Ser2719fs (c.8155_8156del) is associated with Median cleft lip and palate, polydactyly (ClinVar).

How common is CPLANE1 p.Ser2719fs (c.8155_8156del) in the general population?

CPLANE1 p.Ser2719fs (c.8155_8156del) is absent from gnomAD (gnomAD).

CPLANE1 p.Ser2719fs

c.8155_8156del · rs1774291665 · VCV978622

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

Median cleft lip and palate

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 42 of 53
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.9	GERP -0.16, phastCons 0.14

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.Ser2719fs
Coding: c.8155_8156del
MANE Select: NM_001384732
dbSNP: rs1774291665
Type: Microsatellite
Location: chr5:37153957 (GRCh38)
Gene constraint: LOEUF 0.728 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 2719: a UniProt-annotated variant site (in ofd6; likely pathogenic)

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

Disease context

Median cleft lip and palate — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: polydactyly

Similar variants

CPLANE1 p.Pro1236fs Likely pathogenic ★ same condition
CPLANE1 p.Trp1020fs Pathogenic/Likely pathogenic ★★ same type
CPLANE1 p.Val2090fs Pathogenic ★★ same type
CPLANE1 c.5819_5820+1del Uncertain significance ★★ same type
CPLANE1 p.Glu3167fs Uncertain significance ★★ same type
CPLANE1 c.938+19_938+22del Likely benign ★★ same type
CPLANE1 p.Arg400fs Pathogenic ★ same type
CPLANE1 p.Leu1213fs 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-ser2719fs (accessed [today's date]).

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