Is PLEC p.Ala2610= (c.7830G>A) pathogenic?

PLEC p.Ala2610= (c.7830G>A) is classified Conflicting classifications of pathogenicity in PLEC (ClinVar, Conflicting submitters, 9 submitters; last evaluated 2026-02-27). Rare (popmax 0.285%, afr); Associated with epidermolysis bullosa simplex 5A, Ogna type.

What condition is associated with PLEC p.Ala2610= (c.7830G>A)?

PLEC p.Ala2610= (c.7830G>A) is associated with epidermolysis bullosa simplex 5A, Ogna type, epidermolysis bullosa simplex 5B, with muscular dystrophy, epidermolysis bullosa simplex 5C, with pyloric atresia (ClinVar).

How common is PLEC p.Ala2610= (c.7830G>A) in the general population?

PLEC p.Ala2610= (c.7830G>A) is rare (popmax 0.285%, afr) (gnomAD).

PLEC p.Ala2610=

Q: How is PLEC-related intermediate epidermolysis bullosa simplex without extracutaneous involvement inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

c.7830G>A · rs376112916 · VCV167506

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 9 submitters

gnomAD v4.1

Rare

rare (popmax 0.285%, afr)

Conditions

epidermolysis bullosa simplex 5A, Ogna type

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.006	strongly benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -15
Overall
CADD	0.018	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.285% African / African-American · 214/75,048 alleles

Filtering AF 0.254% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.242%

Overall 0.0243% 388/1,598,492 alleles · rare exomes 246/1,446,120 · genomes 142/152,372 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.285%	351
Middle Eastern	0.0837%	1,194
Admixed American	0.0317%	3,157
Remaining individualsnot grpmax-eligible	0.0257%	3,896
European (non-Finnish)	0.0107%	9,363
South Asian	0.00549%	18,199
Finnishnot grpmax-eligible	0.00407%	24,558
East Asian	0.00223%	44,874

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.Ala2610=
Coding: c.7830G>A
MANE Select: NM_201384
dbSNP: rs376112916
Type: single nucleotide variant
Location: chr8:143921991 (GRCh38)
Gene constraint: LOEUF 0.726 · pLI <0.01 (gnomAD)
Residue 2610: 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 5A, Ogna type — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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

For PLEC-related intermediate epidermolysis bullosa simplex without extracutaneous involvement (Orphanet):

Inheritance: Autosomal dominant
Onset: Infancy, Neonatal

Similar variants

PLEC p.Ala2610Val Uncertain significance ★★ ⚠ 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-ala2610 (accessed [today's date]).

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