Is ECI2 p.Pro25Leu (c.74C>T) pathogenic?

ECI2 p.Pro25Leu (c.74C>T) is classified Uncertain significance in ECI2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-30). AlphaMissense: likely benign (0.1512); Very rare (popmax 0.00433%, nfe).

How common is ECI2 p.Pro25Leu (c.74C>T) in the general population?

ECI2 p.Pro25Leu (c.74C>T) is very rare (popmax 0.00433%, nfe) (gnomAD).

What do computational predictors say about ECI2 p.Pro25Leu (c.74C>T)?

AlphaMissense predicts likely benign (score 0.1512) — an in-silico prediction, not a clinical call.

ECI2 p.Pro25Leu

c.74C>T · VCV4246392

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1512 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00433%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1512	likely benign
REVEL	0.078	moderately benign-leaning
SaProt	LLR -6.49	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.22 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.95	GERP -2.4, phastCons 0.6
Regional constraint	o/e 0.99	unconstrained · MANE · 20 kb · p 0.84 · regional, not allelic
Overall
CADD	14.48	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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 0.00433% European (non-Finnish) · 51/1,179,138 alleles

Filtering AF 0.00334% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00302%

Overall 0.00335% 54/1,611,144 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00433%	23,120
African / African-American	0.00401%	24,912

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: ECI2
Protein: p.Pro25Leu
Coding: c.74C>T
MANE Select: NM_206836
Type: single nucleotide variant
Location: chr6:4133688 (GRCh38)
Gene constraint: LOEUF 0.949 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.40 · 5 PDB

Full ECI2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ECI2 p.Pro25Arg Uncertain significance ★ ⚠ same residue
ECI2 p.Ala11Pro Uncertain significance ★ ⚠ same type
ECI2 p.Ala67Thr Uncertain significance ★ ⚠ same type
ECI2 p.Ala67Val Uncertain significance ★ ⚠ same type
ECI2 p.Ala7Val Uncertain significance ★ ⚠ same type
ECI2 p.Ala95Thr Uncertain significance ★ ⚠ same type
ECI2 p.Arg157Trp Uncertain significance ★ same type
ECI2 p.Cys15Tyr Uncertain significance ★ ⚠ same type

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/eci2-p-pro25leu (accessed [today's date]).

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