Is CHST14 p.Lys89fs (c.264del) pathogenic?

CHST14 p.Lys89fs (c.264del) is classified Pathogenic in CHST14 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-31). No allele count reported in gnomAD v4.1 (AN 1,595,206); Associated with Ehlers-Danlos syndrome, musculocontractural type.

What condition is associated with CHST14 p.Lys89fs (c.264del)?

CHST14 p.Lys89fs (c.264del) is associated with Ehlers-Danlos syndrome, musculocontractural type (ClinVar).

How common is CHST14 p.Lys89fs (c.264del) in the general population?

CHST14 p.Lys89fs (c.264del) is no allele count reported in gnomAD v4.1 (AN 1,595,206) (gnomAD).

How is Musculocontractural Ehlers-Danlos syndrome inherited?

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

CHST14 p.Lys89fs

c.264del · rs2543005630 · VCV1949857

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,595,206)

Conditions

Ehlers-Danlos syndrome, musculocontractural type

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (1 of 1) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.5	GERP 1.4, phastCons 0.002

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,595,206). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CHST14
Protein: p.Lys89fs
Coding: c.264del
MANE Select: NM_130468
dbSNP: rs2543005630
Type: Deletion
Location: chr15:40471473 (GRCh38)
Gene constraint: LOEUF 0.917 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.17

Full CHST14 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

For Musculocontractural Ehlers-Danlos syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

CHST14 p.Leu58fs Pathogenic/Likely pathogenic ★★ same condition
CHST14 p.Ser252fs Pathogenic/Likely pathogenic ★★ same condition
CHST14 p.Ser53fs Pathogenic/Likely pathogenic ★★ same condition
CHST14 p.Ala30fs Pathogenic ★ same condition
CHST14 p.Arg244fs Pathogenic ★ same condition
CHST14 p.Gln106fs Pathogenic ★ same condition
CHST14 p.Glu262fs Pathogenic ★ same condition
CHST14 p.Val165fs 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/chst14-p-lys89fs (accessed [today's date]).

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