Is EFEMP2 p.Ser137Cys (c.409A>T) pathogenic?

EFEMP2 p.Ser137Cys (c.409A>T) is classified Conflicting classifications of pathogenicity in EFEMP2 (ClinVar, Conflicting submitters, 5 submitters; last evaluated 2025-11-03). AlphaMissense: likely pathogenic (0.8887); Rare (popmax 0.112%, amr); Associated with Cardiovascular phenotype.

What condition is associated with EFEMP2 p.Ser137Cys (c.409A>T)?

EFEMP2 p.Ser137Cys (c.409A>T) is associated with Cardiovascular phenotype, cutis laxa, autosomal recessive, type 1B (ClinVar).

How common is EFEMP2 p.Ser137Cys (c.409A>T) in the general population?

EFEMP2 p.Ser137Cys (c.409A>T) is rare (popmax 0.112%, amr) (gnomAD).

What do computational predictors say about EFEMP2 p.Ser137Cys (c.409A>T)?

AlphaMissense predicts likely pathogenic (score 0.8887) — an in-silico prediction, not a clinical call.

EFEMP2 p.Ser137Cys

c.409A>T · rs1306393544 · VCV472824

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 5 submitters

AlphaMissense

likely pathogenic

0.8887 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.112%, amr)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.8887	likely pathogenic
REVEL	0.716	pathogenic-leaning
SaProt	LLR -11.18	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 7.8	GERP 0.91, phastCons 1
Regional constraint	o/e 0.83	unconstrained · MANE · 5,433 bp · p 3.8e-05 · regional, not allelic
Overall
CADD	28.9	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.112% Admixed American · 67/59,984 alleles

Filtering AF 0.0902% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0824%

Overall 0.00428% 69/1,613,922 alleles · rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.112%	895
Remaining individualsnot grpmax-eligible	0.0016%	62,484
African / African-American	0.00134%	74,880

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: EFEMP2
Protein: p.Ser137Cys
Coding: c.409A>T
MANE Select: NM_016938
dbSNP: rs1306393544
Type: single nucleotide variant
Location: chr11:65870617 (GRCh38)
Gene constraint: LOEUF 0.56 · pLI 0.62 (gnomAD)
Structure: AlphaFold pLDDT 82.95 · 1 PDB
Residue 137: a disulfide bond; the egf-like 2; calcium-binding domain

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

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: cutis laxa, autosomal recessive, type 1B

Similar variants

EFEMP2 p.Arg279Cys Likely pathogenic ★★ same condition
EFEMP2 p.Asp203Ala Pathogenic/Likely pathogenic ★★ same condition
EFEMP2 p.Glu126Lys Pathogenic/Likely pathogenic ★★ same condition
EFEMP2 p.Glu161Lys Pathogenic/Likely pathogenic ★★ ⚠ same condition
EFEMP2 p.Glu167Ter Pathogenic ★★ same condition
EFEMP2 c.161-6C>G Uncertain significance ★★ same condition
EFEMP2 c.491-5C>G Uncertain significance ★★ same condition
EFEMP2 c.608-3C>G 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/efemp2-p-ser137cys (accessed [today's date]).

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