Is EVC p.Ser263fs (c.787_788delinsA) pathogenic?

EVC p.Ser263fs (c.787788delinsA) is classified Likely pathogenic in EVC (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-02). No gnomAD frequency available for this variant; Associated with Ellis-van Creveld syndrome.

What condition is associated with EVC p.Ser263fs (c.787_788delinsA)?

EVC p.Ser263fs (c.787_788delinsA) is associated with Ellis-van Creveld syndrome (ClinVar).

How common is EVC p.Ser263fs (c.787_788delinsA) in the general population?

EVC p.Ser263fs (c.787_788delinsA) is no gnomAD frequency available for this variant (gnomAD).

EVC p.Ser263fs

c.787_788delinsA · rs2474947769 · VCV1724246

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

Ellis-van Creveld syndrome

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 6 of 21
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.2	GERP 1.7, phastCons 0.96

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: EVC
Protein: p.Ser263fs
Coding: c.787_788delinsA
MANE Select: NM_153717
dbSNP: rs2474947769
Type: Indel
Location: chr4:5741800 (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.Ser263Ter Pathogenic ★ same residue
EVC p.Glu420fs Pathogenic/Likely pathogenic ★★ same condition
EVC c.2562-13_2562-12delinsCC Likely benign ★★ same condition
EVC p.Arg935fs Likely pathogenic ★ same condition
EVC p.Gln361fs Likely pathogenic ★ same condition
EVC p.Gln878_Gln879delinsHisTer Pathogenic ★ same condition
EVC p.His454fs Likely pathogenic ★ same condition
EVC p.Lys301fs 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-ser263fs (accessed [today's date]).

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