Is ECEL1 p.Val558fs (c.1672del) pathogenic?

ECEL1 p.Val558fs (c.1672del) is classified Pathogenic in ECEL1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-16). Absent from gnomAD; Associated with distal arthrogryposis type 5D.

What condition is associated with ECEL1 p.Val558fs (c.1672del)?

ECEL1 p.Val558fs (c.1672del) is associated with distal arthrogryposis type 5D (ClinVar).

How common is ECEL1 p.Val558fs (c.1672del) in the general population?

ECEL1 p.Val558fs (c.1672del) is absent from gnomAD (gnomAD).

How is Distal arthrogryposis type 5D inherited?

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

ECEL1 p.Val558fs

c.1672del · rs2469642191 · VCV1706601

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

distal arthrogryposis type 5D

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 10 of 18
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.2	GERP 5.5, phastCons 1

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: ECEL1
Protein: p.Val558fs
Coding: c.1672del
MANE Select: NM_004826
dbSNP: rs2469642191
Type: Deletion
Location: chr2:232482864 (GRCh38)
Gene constraint: LOEUF 1.099 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.62
Residue 558: a disulfide bond; the peptidase m13 domain

Full ECEL1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

distal arthrogryposis type 5D — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Distal arthrogryposis type 5D (Orphanet):

Inheritance: Autosomal recessive
Onset: Neonatal

Similar variants

ECEL1 p.Gly170fs Pathogenic ★★ same condition
ECEL1 p.Gly27fs Pathogenic/Likely pathogenic ★★ same condition
ECEL1 p.Phe37fs Pathogenic ★★ same condition
ECEL1 p.Arg49_Ser50delinsPro Likely pathogenic ★ same condition
ECEL1 p.Gln348fs Pathogenic ★ same condition
ECEL1 p.Glu13fs Likely pathogenic ★ same condition
ECEL1 p.Gly133fs Likely pathogenic ★ same condition
ECEL1 p.Pro595_Asp596del Likely 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/ecel1-p-val558fs (accessed [today's date]).

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