Is ECEL1 p.Val88= (c.264C>G) pathogenic?

ECEL1 p.Val88= (c.264C>G) is classified Likely benign in ECEL1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-12-11). Absent from gnomAD v4.1; Associated with ECEL1-related disorder.

What condition is associated with ECEL1 p.Val88= (c.264C>G)?

ECEL1 p.Val88= (c.264C>G) is associated with ECEL1-related disorder (ClinVar).

How common is ECEL1 p.Val88= (c.264C>G) in the general population?

ECEL1 p.Val88= (c.264C>G) is absent from gnomAD v4.1 (gnomAD).

ECEL1 p.Val88=

c.264C>G · rs1397958331 · VCV3030732

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

ECEL1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.017	GERP -2.3
Overall
CADD	1.468	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ECEL1
Protein: p.Val88=
Coding: c.264C>G
MANE Select: NM_004826
dbSNP: rs1397958331
Type: single nucleotide variant
Location: chr2:232486390 (GRCh38)
Gene constraint: LOEUF 1.099 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.62

Full ECEL1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ECEL1-related disorder

Similar variants

ECEL1 p.Gln435Ter Pathogenic/Likely pathogenic ★★ same condition
ECEL1 p.Thr615Pro Likely pathogenic ★ same condition
ECEL1 p.Tyr618Ter Likely pathogenic ★ same condition
ECEL1 p.Val385= Likely pathogenic ★ same condition
ECEL1 p.Arg404Cys Conflicting classifications of pathogenicity ★ ⚠ same condition
ECEL1 p.Leu733Pro Uncertain significance ★ ⚠ same condition
ECEL1 p.Arg663Trp Uncertain significance ⚠ same condition
ECEL1 c.2228+4T>A Likely benign 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/ecel1-p-val88 (accessed [today's date]).

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