Is ECEL1 p.Phe37fs (c.110_155del) pathogenic?

ECEL1 p.Phe37fs (c.110155del) is classified Pathogenic in ECEL1 (ClinVar, Multiple submitters, 10 submitters; last evaluated 2026-06-01). Ultra-rare (popmax 0.0551%, amr); Associated with Inborn genetic diseases.

What condition is associated with ECEL1 p.Phe37fs (c.110_155del)?

ECEL1 p.Phe37fs (c.110_155del) is associated with Inborn genetic diseases, distal arthrogryposis type 5D (ClinVar).

How common is ECEL1 p.Phe37fs (c.110_155del) in the general population?

ECEL1 p.Phe37fs (c.110_155del) is ultra-rare (popmax 0.0551%, amr) (gnomAD).

ECEL1 p.Phe37fs

c.110_155del · rs1341894581 · VCV435024

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 10 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

ultra-rare (popmax 0.0551%, amr)

Conditions

Inborn genetic diseases

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 2 of 18
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.4	GERP -1.6, phastCons 0.99
Overall
CADD	33.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0551% Admixed American · 15/27,218 alleles

Filtering AF 0.0339% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0274%

Overall 0.00571% 79/1,383,780 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0551%	1,815
African / African-American	0.00612%	16,335
Remaining individualsnot grpmax-eligible	0.00569%	17,568
European (non-Finnish)	0.0051%	19,619
East Asian	0.00309%	32,396
South Asian	0.00167%	59,904

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: ECEL1
Protein: p.Phe37fs
Coding: c.110_155del
MANE Select: NM_004826
dbSNP: rs1341894581
Type: Deletion
Location: chr2:232486499 (GRCh38)
Gene constraint: LOEUF 1.099 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.62

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: distal arthrogryposis type 5D

Similar variants

ECEL1 p.Phe37Cys Uncertain significance ★ ⚠ same residue
ECEL1 p.Gly170fs Pathogenic ★★ same condition
ECEL1 p.Gly27fs Pathogenic/Likely 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-phe37fs (accessed [today's date]).

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