Is PLEC p.Glu1663del (c.4987_4989del) pathogenic?

PLEC p.Glu1663del (c.49874989del) is classified Uncertain significance in PLEC (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-18). No gnomAD frequency available for this variant; Associated with epidermolysis bullosa simplex with nail dystrophy.

What condition is associated with PLEC p.Glu1663del (c.4987_4989del)?

PLEC p.Glu1663del (c.4987_4989del) is associated with epidermolysis bullosa simplex with nail dystrophy, epidermolysis bullosa simplex 5A, Ogna type, epidermolysis bullosa simplex 5B, with muscular dystrophy (ClinVar).

How common is PLEC p.Glu1663del (c.4987_4989del) in the general population?

PLEC p.Glu1663del (c.4987_4989del) is no gnomAD frequency available for this variant (gnomAD).

PLEC p.Glu1663del

c.4987_4989del · rs1824427429 · VCV2929208

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

epidermolysis bullosa simplex with nail dystrophy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.1	phastCons 1

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: PLEC
Protein: p.Glu1663del
Coding: c.4987_4989del
MANE Select: NM_201384
dbSNP: rs1824427429
Type: Deletion
Location: chr8:143924940 (GRCh38)
Gene constraint: LOEUF 0.726 · pLI <0.01 (gnomAD)
Residue 1663: the 'required for interaction with intermediate filament proteins' region; the 'central fibrous rod domain' region

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

Disease context

epidermolysis bullosa simplex with nail dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: epidermolysis bullosa simplex 5A, Ogna type epidermolysis bullosa simplex 5B, with muscular dystrophy epidermolysis bullosa simplex 5C, with pyloric atresia autosomal recessive limb-girdle muscular dystrophy type 2Q

Similar variants

PLEC p.Asn489fs Pathogenic ★★ same condition
PLEC p.Glu3188fs Pathogenic ★★ same condition
PLEC p.Ala4499_Arg4502del Uncertain significance ★★ same condition
PLEC p.Glu4123del Uncertain significance ★★ same condition
PLEC p.Ser2284_Leu2293del Uncertain significance ★★ same condition
PLEC c.1815+18del Likely benign ★★ same condition
PLEC c.2305-10del Benign/Likely benign ★★ same condition
PLEC c.2305-11del Benign/Likely benign ★★ 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/plec-p-glu1663del (accessed [today's date]).

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