Is PLEC p.Ser3315= (c.9945C>T) pathogenic?

PLEC p.Ser3315= (c.9945C>T) is classified Benign in PLEC (ClinVar, Multiple submitters, 8 submitters; last evaluated 2026-02-01). Low-frequency (popmax 4.14%, afr); Associated with epidermolysis bullosa simplex 5A, Ogna type.

What condition is associated with PLEC p.Ser3315= (c.9945C>T)?

PLEC p.Ser3315= (c.9945C>T) 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.Ser3315= (c.9945C>T) in the general population?

PLEC p.Ser3315= (c.9945C>T) is low-frequency (popmax 4.14%, afr) (gnomAD).

PLEC p.Ser3315=

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.9945C>T · rs28657061 · VCV93015

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 8 submitters

gnomAD v4.1

Rare

low-frequency (popmax 4.14%, 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.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -8.4
Overall
CADD	0.434	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 4.14% African / African-American · 3,105/75,042 alleles

Filtering AF 4.02% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.97%

Overall 0.575% 9,277/1,613,086 alleles · low-frequency exomes 6,956/1,460,750 · genomes 2,321/152,336 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	4.14%	24
Middle Eastern	0.99%	101
Admixed American	0.923%	108
Remaining individualsnot grpmax-eligible	0.69%	145
Ashkenazi Jewishnot grpmax-eligible	0.588%	170
European (non-Finnish)	0.407%	246
Finnishnot grpmax-eligible	0.216%	463
South Asian	0.0154%	6,506
East Asian	0.00446%	22,443

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.Ser3315=
Coding: c.9945C>T
MANE Select: NM_201384
dbSNP: rs28657061
Type: single nucleotide variant
Location: chr8:143919876 (GRCh38)
Gene constraint: LOEUF 0.726 · pLI <0.01 (gnomAD)
Residue 3315: the 'required for interaction with intermediate filament proteins' region; the 'globular 2' region; the 'disordered' 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.Ser3315Asn Uncertain significance ★ ⚠ same residue
PLEC p.Ser3315Gly 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

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-ser3315 (accessed [today's date]).

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