Is ECEL1 p.Ser256Phe (c.767C>T) pathogenic?

ECEL1 p.Ser256Phe (c.767C>T) is classified Uncertain significance in ECEL1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-24). AlphaMissense: likely pathogenic (0.961); Ultra-rare (popmax 0.0163%, afr); Associated with Inborn genetic diseases.

What condition is associated with ECEL1 p.Ser256Phe (c.767C>T)?

ECEL1 p.Ser256Phe (c.767C>T) is associated with Inborn genetic diseases (ClinVar).

How common is ECEL1 p.Ser256Phe (c.767C>T) in the general population?

ECEL1 p.Ser256Phe (c.767C>T) is ultra-rare (popmax 0.0163%, afr) (gnomAD).

What do computational predictors say about ECEL1 p.Ser256Phe (c.767C>T)?

AlphaMissense predicts likely pathogenic (score 0.961) — an in-silico prediction, not a clinical call.

ECEL1 p.Ser256Phe

c.767C>T · VCV4016007

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.961 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0163%, afr)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.961	likely pathogenic
REVEL	0.825	moderately pathogenic-leaning
SaProt	LLR -11.55	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.5, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 6,497 bp · p 0.15 · regional, not allelic
Overall
CADD	32.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0163% African / African-American · 12/73,772 alleles

Filtering AF 0.00935% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00732%

Overall 0.000961% 15/1,561,296 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0163%	6,148
Remaining individualsnot grpmax-eligible	0.0033%	30,330
Admixed American	0.00188%	53,144

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: ECEL1
Protein: p.Ser256Phe
Coding: c.767C>T
MANE Select: NM_004826
Type: single nucleotide variant
Location: chr2:232485887 (GRCh38)
Gene constraint: LOEUF 1.099 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.62
Residue 256: a disulfide bond; the peptidase m13 domain

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ECEL1 p.Ser256= Benign ★ same residue
ECEL1 p.Arg756Trp Uncertain significance ★★ ⚠ same condition
ECEL1 p.Gly209Val Uncertain significance ★★ ⚠ same condition
ECEL1 p.Pro34Ser Uncertain significance ★★ ⚠ same condition
ECEL1 p.Ser44Arg Uncertain significance ★★ ⚠ same condition
ECEL1 p.Arg355Gln Likely benign ★★ same condition
ECEL1 c.1990-6C>T Conflicting classifications of pathogenicity ★ same condition
ECEL1 p.Ala109Val Uncertain significance ★ ⚠ 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-ser256phe (accessed [today's date]).

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