Is EFEMP2 p.Asp46= (c.138C>T) pathogenic?

EFEMP2 p.Asp46= (c.138C>T) is classified Benign/Likely benign in EFEMP2 (ClinVar, Multiple submitters, 8 submitters; last evaluated 2026-01-25). Low-frequency (popmax 1.18%, afr); Associated with Cardiovascular phenotype.

What condition is associated with EFEMP2 p.Asp46= (c.138C>T)?

EFEMP2 p.Asp46= (c.138C>T) is associated with Cardiovascular phenotype, cutis laxa, autosomal recessive, type 1B (ClinVar).

How common is EFEMP2 p.Asp46= (c.138C>T) in the general population?

EFEMP2 p.Asp46= (c.138C>T) is low-frequency (popmax 1.18%, afr) (gnomAD).

EFEMP2 p.Asp46=

c.138C>T · rs2234457 · VCV472812

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 8 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.18%, afr)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.9	GERP -1.8, phastCons 1
Overall
CADD	10.67	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.18% African / African-American · 863/73,120 alleles

Filtering AF 1.11% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.09%

Overall 0.0637% 988/1,551,630 alleles · low-frequency exomes 460/1,399,402 · genomes 528/152,228 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.18%	85
Admixed American	0.133%	750
Remaining individualsnot grpmax-eligible	0.0815%	1,227
Middle Eastern	0.0167%	5,992
South Asian	0.00119%	84,064
European (non-Finnish)	0.000523%	191,161

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.Asp46=
Coding: c.138C>T
MANE Select: NM_016938
dbSNP: rs2234457
Type: single nucleotide variant
Location: chr11:65871992 (GRCh38)
Gene constraint: LOEUF 0.56 · pLI 0.62 (gnomAD)
Structure: AlphaFold pLDDT 82.95 · 1 PDB
Residue 46: the egf-like 1; atypical 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-asp46 (accessed [today's date]).

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