Is PLEC p.Ala2354= (c.7062G>A) pathogenic?

PLEC p.Ala2354= (c.7062G>A) is classified Conflicting classifications of pathogenicity in PLEC (ClinVar, Conflicting submitters, 7 submitters; last evaluated 2026-01-21). Rare (popmax 0.121%, sas); Associated with epidermolysis bullosa simplex with nail dystrophy.

What condition is associated with PLEC p.Ala2354= (c.7062G>A)?

PLEC p.Ala2354= (c.7062G>A) 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.Ala2354= (c.7062G>A) in the general population?

PLEC p.Ala2354= (c.7062G>A) is rare (popmax 0.121%, sas) (gnomAD).

PLEC p.Ala2354=

c.7062G>A · rs375587611 · VCV196753

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

rare (popmax 0.121%, sas)

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 · no allele here is in the release
Constraint at this position
Conservation	phyloP -16
Overall
CADD	0.005	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.121% South Asian · 106/87,714 alleles

Filtering AF 0.102% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0952%

Overall 0.0805% 1,273/1,580,538 alleles · rare exomes 1,206/1,428,266 · genomes 67/152,272 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.121%	827
European (non-Finnish)	0.0945%	1,059
Remaining individualsnot grpmax-eligible	0.0441%	2,267
Admixed American	0.0216%	4,622
Finnishnot grpmax-eligible	0.0204%	4,906
African / African-American	0.0202%	4,945
Middle Eastern	0.0174%	5,748

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: PLEC
Protein: p.Ala2354=
Coding: c.7062G>A
MANE Select: NM_201384
dbSNP: rs375587611
Type: single nucleotide variant
Location: chr8:143922867 (GRCh38)
Gene constraint: LOEUF 0.726 · pLI <0.01 (gnomAD)
Residue 2354: 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.Ala2354Val Conflicting classifications of pathogenicity ★ ⚠ same residue
PLEC p.Arg1490Ter Pathogenic/Likely pathogenic ★★ same condition
PLEC p.Arg1973Trp Pathogenic ★★ ⚠ same condition
PLEC p.Arg2027Ter Pathogenic ★★ same condition
PLEC p.Arg2292Ter Pathogenic ★★ same condition
PLEC p.Arg2324Ter Pathogenic ★★ same condition
PLEC p.Arg2394Ter Pathogenic ★★ same condition
PLEC p.Arg559Ter Pathogenic ★★ 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-ala2354 (accessed [today's date]).

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