Is ELP1 p.Phe207fs (c.620_621del) pathogenic?

ELP1 p.Phe207fs (c.620621del) is classified Pathogenic in ELP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-17). Associated with Riley-Day syndrome.

What condition is associated with ELP1 p.Phe207fs (c.620_621del)?

ELP1 p.Phe207fs (c.620_621del) is associated with Riley-Day syndrome (ClinVar).

How is Familial dysautonomia inherited?

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

ELP1 p.Phe207fs

c.620_621del · VCV3385235

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

Riley-Day syndrome

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 7 of 37
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.6	GERP 1.4, phastCons 1

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

Variant & gene context

Gene: ELP1
Protein: p.Phe207fs
Coding: c.620_621del
MANE Select: NM_003640
Type: Deletion
Location: chr9:108919281 (GRCh38)
Gene constraint: LOEUF 0.803 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.31 · 5 PDB
Residue 207: a β-strand

Full ELP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Riley-Day syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Familial dysautonomia (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy, Neonatal
Prevalence: <1 / 1 000 000 (Europe)

Similar variants

ELP1 c.2860+1_2860+7del Likely pathogenic ★★ same condition
ELP1 c.2958+1del Likely pathogenic ★★ same condition
ELP1 c.954_958+7del Likely pathogenic ★★ same condition
ELP1 p.Asn225fs Pathogenic/Likely pathogenic ★★ same condition
ELP1 p.Asn384_Ser385insTer Pathogenic/Likely pathogenic ★★ same condition
ELP1 p.Asp495fs Pathogenic/Likely pathogenic ★★ same condition
ELP1 p.Cys319fs Pathogenic/Likely pathogenic ★★ same condition
ELP1 p.Gln577fs Pathogenic/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/elp1-p-phe207fs (accessed [today's date]).

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