Is EVC p.Phe429del (c.1286_1288del) pathogenic?

EVC p.Phe429del (c.12861288del) is classified Uncertain significance in EVC (ClinVar, No assertion criteria, 1 submitter; last evaluated 2017-05-17). No gnomAD frequency available for this variant; Associated with Ellis-van Creveld syndrome.

What condition is associated with EVC p.Phe429del (c.1286_1288del)?

EVC p.Phe429del (c.1286_1288del) is associated with Ellis-van Creveld syndrome (ClinVar).

How common is EVC p.Phe429del (c.1286_1288del) in the general population?

EVC p.Phe429del (c.1286_1288del) is no gnomAD frequency available for this variant (gnomAD).

EVC p.Phe429del

c.1286_1288del · rs1553875733 · VCV551911

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Ellis-van Creveld syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.8	GERP 0.82, phastCons 1

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: EVC
Protein: p.Phe429del
Coding: c.1286_1288del
MANE Select: NM_153717
dbSNP: rs1553875733
Type: Deletion
Location: chr4:5753021 (GRCh38)
Gene constraint: LOEUF 1.134 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.49

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

Disease context

Ellis-van Creveld syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EVC p.Phe429fs Likely pathogenic ★ same residue
EVC p.Phe429= Likely benign ★ same residue
EVC c.1783_1886+40del Pathogenic ★★ same condition
EVC c.1887-5_1904del Pathogenic/Likely pathogenic ★★ same condition
EVC c.2782+1del Pathogenic ★★ same condition
EVC p.Ala565fs Pathogenic ★★ same condition
EVC p.Asn68fs Pathogenic ★★ same condition
EVC p.Asp132fs 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/evc-p-phe429del (accessed [today's date]).

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