Is FERMT1 p.Arg17= (c.51C>T) pathogenic?

FERMT1 p.Arg17= (c.51C>T) is classified Benign in FERMT1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-26). Low-frequency (popmax 1.57%, afr); Associated with Kindler syndrome.

What condition is associated with FERMT1 p.Arg17= (c.51C>T)?

FERMT1 p.Arg17= (c.51C>T) is associated with Kindler syndrome (ClinVar).

How common is FERMT1 p.Arg17= (c.51C>T) in the general population?

FERMT1 p.Arg17= (c.51C>T) is low-frequency (popmax 1.57%, afr) (gnomAD).

How is Kindler epidermolysis bullosa inherited?

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

FERMT1 p.Arg17=

c.51C>T · rs147105196 · VCV711755

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.57%, afr)

Conditions

Kindler syndrome

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 -1.7	GERP -4.4
Overall
CADD	1.293	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.57% African / African-American · 1,175/75,024 alleles

Filtering AF 1.49% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.46%

Overall 0.0811% 1,309/1,614,144 alleles · low-frequency exomes 610/1,461,862 · genomes 699/152,282 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.57%	64
Admixed American	0.0933%	1,072
Remaining individualsnot grpmax-eligible	0.088%	1,136
Middle Eastern	0.033%	3,031
South Asian	0.00329%	30,360
European (non-Finnish)	0.00153%	65,557

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: FERMT1
Protein: p.Arg17=
Coding: c.51C>T
MANE Select: NM_017671
dbSNP: rs147105196
Type: single nucleotide variant
Location: chr20:6119504 (GRCh38)
Gene constraint: LOEUF 0.871 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.14

Full FERMT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Kindler syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Kindler epidermolysis bullosa (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

FERMT1 p.Arg17His Uncertain significance ★★ ⚠ same residue
FERMT1 p.Arg17Cys Uncertain significance ★ ⚠ same residue
FERMT1 c.1371+4A>G Pathogenic ★★ same condition
FERMT1 p.Arg110Ter Pathogenic ★★ same condition
FERMT1 p.Arg271Ter Pathogenic ★★ same condition
FERMT1 p.Arg288Ter Pathogenic ★★ same condition
FERMT1 p.Glu304Ter Pathogenic ★★ same condition
FERMT1 c.*1004G>A Uncertain significance ★★ 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/fermt1-p-arg17 (accessed [today's date]).

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