Is FKBP14 p.Leu32fs (c.95_96del) pathogenic?

FKBP14 p.Leu32fs (c.9596del) is classified Pathogenic in FKBP14 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-08). Very rare (popmax 6.2e-05%); Associated with Ehlers-Danlos syndrome, kyphoscoliotic type, 2.

What condition is associated with FKBP14 p.Leu32fs (c.95_96del)?

FKBP14 p.Leu32fs (c.95_96del) is associated with Ehlers-Danlos syndrome, kyphoscoliotic type, 2 (ClinVar).

How common is FKBP14 p.Leu32fs (c.95_96del) in the general population?

FKBP14 p.Leu32fs (c.95_96del) is very rare (popmax 6.2e-05%) (gnomAD).

FKBP14 p.Leu32fs

c.95_96del · rs2127950876 · VCV1068632

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 6.2e-05%)

Conditions

Ehlers-Danlos syndrome, kyphoscoliotic type, 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 1 of 4
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 2.3, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.2e-05%

Overall 6.2e-05% 1/1,614,176 alleles · very rare exomes 1/1,461,836 · genomes 0/152,340 · joint denominator

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: FKBP14
Protein: p.Leu32fs
Coding: c.95_96del
MANE Select: NM_017946
dbSNP: rs2127950876
Type: Microsatellite
Location: chr7:30026413 (GRCh38)
Gene constraint: LOEUF 1.342 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 88.27 · 2 PDB
Residue 32: a β-strand

Full FKBP14 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Ehlers-Danlos syndrome, kyphoscoliotic type, 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Kyphoscoliotic Ehlers-Danlos syndrome (Orphanet):

Onset: Antenatal, Neonatal

Similar variants

FKBP14 c.197+5_197+8del Likely pathogenic ★ same condition
FKBP14 p.Asn176fs Likely pathogenic ★ same condition
FKBP14 p.Leu12fs Pathogenic ★ same condition
FKBP14 p.Leu155_Ser156insTer Conflicting classifications of pathogenicity ★ same condition
FKBP14 p.Lys166del Conflicting classifications of pathogenicity ★ same condition
FKBP14 p.Ter212GluextTer? Uncertain significance ★ same condition
FKBP14 c.477+15_477+17del Likely benign ★ same condition
FKBP14 p.Glu191del 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/fkbp14-p-leu32fs (accessed [today's date]).

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