Is PLEC p.Arg1797= (c.5391C>T) pathogenic?

PLEC p.Arg1797= (c.5391C>T) is classified Conflicting classifications of pathogenicity in PLEC (ClinVar, Conflicting submitters, 8 submitters; last evaluated 2026-02-01). Rare (popmax 0.464%, amr); Associated with epidermolysis bullosa simplex with nail dystrophy.

What condition is associated with PLEC p.Arg1797= (c.5391C>T)?

PLEC p.Arg1797= (c.5391C>T) 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.Arg1797= (c.5391C>T) in the general population?

PLEC p.Arg1797= (c.5391C>T) is rare (popmax 0.464%, amr) (gnomAD).

PLEC p.Arg1797=

c.5391C>T · rs551187778 · VCV196732

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 8 submitters

gnomAD v4.1

Rare

rare (popmax 0.464%, amr)

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 -9.4
Overall
CADD	0.508	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.464% Admixed American · 243/52,378 alleles

Filtering AF 0.416% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.397%

Overall 0.12% 1,843/1,538,762 alleles · rare exomes 1,676/1,387,326 · genomes 167/151,436 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.464%	216
Remaining individualsnot grpmax-eligible	0.137%	730
European (non-Finnish)	0.125%	801
Ashkenazi Jewishnot grpmax-eligible	0.102%	983
African / African-American	0.0388%	2,578
South Asian	0.0259%	3,857
East Asian	0.00493%	20,304
Finnishnot grpmax-eligible	0.0045%	22,211

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.Arg1797=
Coding: c.5391C>T
MANE Select: NM_201384
dbSNP: rs551187778
Type: single nucleotide variant
Location: chr8:143924538 (GRCh38)
Gene constraint: LOEUF 0.726 · pLI <0.01 (gnomAD)
Residue 1797: the 'required for interaction with intermediate filament proteins' region; the 'central fibrous rod domain' region; the 'disordered' 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.Arg1797His Uncertain significance ★★ same residue
PLEC p.Arg1797Cys 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

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-arg1797 (accessed [today's date]).

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