Is EMILIN2 p.Pro390Ser (c.1168C>T) pathogenic?

EMILIN2 p.Pro390Ser (c.1168C>T) is classified Uncertain significance in EMILIN2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-28). AlphaMissense: likely benign (0.0881); Absent from gnomAD v4.1.

How common is EMILIN2 p.Pro390Ser (c.1168C>T) in the general population?

EMILIN2 p.Pro390Ser (c.1168C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EMILIN2 p.Pro390Ser (c.1168C>T)?

AlphaMissense predicts likely benign (score 0.0881) — an in-silico prediction, not a clinical call.

EMILIN2 p.Pro390Ser

c.1168C>T · rs2510221942 · VCV3088601

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0881 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0881	likely benign
REVEL	0.113	moderately benign-leaning
SaProt	LLR -7.42	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 1.7	GERP 1.4, phastCons 0.68
Regional constraint	o/e 1.03	unconstrained · MANE · 66 kb · p 0.34 · regional, not allelic
Overall
CADD	16.89	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

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: EMILIN2
Protein: p.Pro390Ser
Coding: c.1168C>T
MANE Select: NM_032048
dbSNP: rs2510221942
Type: single nucleotide variant
Location: chr18:2891295 (GRCh38)
Gene constraint: LOEUF 1.047 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 65.88

Full EMILIN2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EMILIN2 p.Ala215Thr Benign ★★ same type
EMILIN2 p.Ala455= Benign ★★ same type
EMILIN2 p.Cys1002= Benign ★★ same type
EMILIN2 p.Gly843= Benign/Likely benign ★★ same type
EMILIN2 p.Lys347= Benign ★★ same type
EMILIN2 p.Met259Val Benign ★★ same type
EMILIN2 p.Pro136Ser Benign ★★ same type
EMILIN2 p.Pro657= Benign ★★ 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/emilin2-p-pro390ser (accessed [today's date]).

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