Is EVC p.Leu296fs (c.886del) pathogenic?

EVC p.Leu296fs (c.886del) is classified Likely pathogenic in EVC (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-01). Associated with EVC-related disorder.

What condition is associated with EVC p.Leu296fs (c.886del)?

EVC p.Leu296fs (c.886del) is associated with EVC-related disorder (ClinVar).

EVC p.Leu296fs

c.886del · VCV4966257

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

EVC-related disorder

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 21
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.98	GERP -1.4, phastCons 0.003

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: EVC
Protein: p.Leu296fs
Coding: c.886del
MANE Select: NM_153717
Type: Deletion
Location: chr4:5745286 (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

EVC-related disorder

Similar variants

EVC c.1887-5_1904del Pathogenic/Likely pathogenic ★★ same condition
EVC p.Thr658fs Pathogenic/Likely pathogenic ★★ same condition
EVC p.Leu296= Likely benign ★ same residue
EVC c.384+5G>C Pathogenic/Likely pathogenic ★★ same condition
EVC p.Arg304fs Pathogenic/Likely pathogenic ★★ same condition
EVC p.Arg340Ter Pathogenic/Likely pathogenic ★★ same condition
EVC p.Gln390Ter Pathogenic/Likely pathogenic ★★ same condition
EVC p.Gln879Ter 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-leu296fs (accessed [today's date]).

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