Is EFEMP2 p.Leu81Pro (c.242T>C) pathogenic?

EFEMP2 p.Leu81Pro (c.242T>C) is classified Uncertain significance in EFEMP2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2018-09-16). AlphaMissense: likely pathogenic (0.9937); Absent from gnomAD v4.1.

How common is EFEMP2 p.Leu81Pro (c.242T>C) in the general population?

EFEMP2 p.Leu81Pro (c.242T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EFEMP2 p.Leu81Pro (c.242T>C)?

AlphaMissense predicts likely pathogenic (score 0.9937) — an in-silico prediction, not a clinical call.

EFEMP2 p.Leu81Pro

c.242T>C · rs1565274500 · VCV591856

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9937 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9937	likely pathogenic
REVEL	0.822	moderately pathogenic-leaning
SaProt	LLR -13.27	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 11	GERP 0.85, phastCons 1
Regional constraint	o/e 0.83	unconstrained · MANE · 5,433 bp · p 3.8e-05 · regional, not allelic
Overall
CADD	29.5	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

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: EFEMP2
Protein: p.Leu81Pro
Coding: c.242T>C
MANE Select: NM_016938
dbSNP: rs1565274500
Type: single nucleotide variant
Location: chr11:65871282 (GRCh38)
Gene constraint: LOEUF 0.56 · pLI 0.62 (gnomAD)
Structure: AlphaFold pLDDT 82.95 · 1 PDB
Residue 81: a disulfide bond; the egf-like 1; atypical domain; a β-strand

Full EFEMP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EFEMP2 p.Arg279Cys Likely pathogenic ★★ same type
EFEMP2 p.Arg337Ter Pathogenic/Likely pathogenic ★★ same type
EFEMP2 p.Asp203Ala Pathogenic/Likely pathogenic ★★ same type
EFEMP2 p.Glu126Lys Pathogenic/Likely pathogenic ★★ same type
EFEMP2 p.Glu161Lys Pathogenic/Likely pathogenic ★★ ⚠ same type
EFEMP2 p.Glu167Ter Pathogenic ★★ same type
EFEMP2 c.161-6C>G Uncertain significance ★★ same type
EFEMP2 c.491-5C>G 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/efemp2-p-leu81pro (accessed [today's date]).

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