Is ECI1 p.Pro51Arg (c.152C>G) pathogenic?

ECI1 p.Pro51Arg (c.152C>G) is classified Uncertain significance in ECI1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-01-26). AlphaMissense: likely benign (0.119); Absent from gnomAD v4.1.

How common is ECI1 p.Pro51Arg (c.152C>G) in the general population?

ECI1 p.Pro51Arg (c.152C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ECI1 p.Pro51Arg (c.152C>G)?

AlphaMissense predicts likely benign (score 0.119) — an in-silico prediction, not a clinical call.

ECI1 p.Pro51Arg

c.152C>G · rs890177950 · VCV2272852

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.119 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,237,040)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.119	likely benign
REVEL	0.174	moderately benign-leaning
SaProt	LLR -7.41	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.8	GERP -2.2, phastCons 0.97
Regional constraint	o/e 1.08	unconstrained · MANE · 12 kb · p 0.1 · regional, not allelic
Overall
CADD	16.0	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

No allele count reported in gnomAD v4.1 (AN 1,237,040). 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: ECI1
Protein: p.Pro51Arg
Coding: c.152C>G
MANE Select: NM_001919
dbSNP: rs890177950
Type: single nucleotide variant
Location: chr16:2251330 (GRCh38)
Gene constraint: LOEUF 1.485 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.43 · 1 PDB
Residue 51: a β-strand

Full ECI1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ECI1 p.Thr76Met Benign ★★ same type
ECI1 p.Ala119Thr Uncertain significance ★ ⚠ same type
ECI1 p.Ala185Ser Uncertain significance ★ ⚠ same type
ECI1 p.Ala19Ser Uncertain significance ★ ⚠ same type
ECI1 p.Ala201Val Uncertain significance ★ ⚠ same type
ECI1 p.Ala202Val Uncertain significance ★ same type
ECI1 p.Ala2Val Uncertain significance ★ ⚠ same type
ECI1 p.Ala32Thr 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/eci1-p-pro51arg (accessed [today's date]).

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