Is FKBP14 p.Phe13= (c.39C>T) pathogenic?

FKBP14 p.Phe13= (c.39C>T) is classified Likely benign in FKBP14 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-09-17). Very rare (popmax 0.00288%, nfe); Associated with Cardiovascular phenotype.

What condition is associated with FKBP14 p.Phe13= (c.39C>T)?

FKBP14 p.Phe13= (c.39C>T) is associated with Cardiovascular phenotype, Ehlers-Danlos syndrome, kyphoscoliotic type, 2 (ClinVar).

How common is FKBP14 p.Phe13= (c.39C>T) in the general population?

FKBP14 p.Phe13= (c.39C>T) is very rare (popmax 0.00288%, nfe) (gnomAD).

FKBP14 p.Phe13=

c.39C>T · rs371838963 · VCV1113800

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00288%, nfe)

Conditions

Cardiovascular phenotype

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Pangolin	Δ0.31	gain · loss 0.00 · independent
Constraint at this position
Conservation	phyloP -2.3	GERP -3.5
Overall
CADD	4.38	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00288% European (non-Finnish) · 34/1,179,902 alleles

Filtering AF 0.00207% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00183%

Overall 0.00217% 35/1,613,874 alleles · very rare exomes 35/1,461,558 · genomes 0/152,316 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00288%	34,703
Remaining individualsnot grpmax-eligible	0.0016%	62,482

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.Phe13=
Coding: c.39C>T
MANE Select: NM_017946
dbSNP: rs371838963
Type: single nucleotide variant
Location: chr7:30026470 (GRCh38)

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

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Ehlers-Danlos syndrome, kyphoscoliotic type, 2

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-phe13 (accessed [today's date]).

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