Is ECEL1 p.Phe37Cys (c.110T>G) pathogenic?

ECEL1 p.Phe37Cys (c.110T>G) is classified Uncertain significance in ECEL1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-26). AlphaMissense: ambiguous (0.3453); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with ECEL1 p.Phe37Cys (c.110T>G)?

ECEL1 p.Phe37Cys (c.110T>G) is associated with Inborn genetic diseases (ClinVar).

How common is ECEL1 p.Phe37Cys (c.110T>G) in the general population?

ECEL1 p.Phe37Cys (c.110T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ECEL1 p.Phe37Cys (c.110T>G)?

AlphaMissense predicts ambiguous (score 0.3453) — an in-silico prediction, not a clinical call.

ECEL1 p.Phe37Cys

c.110T>G · rs2469653295 · VCV2374575

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3453 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,341,890)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.3453	ambiguous
REVEL	0.432	indeterminate
SaProt	LLR -5.26	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.1	GERP 0.99, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 6,497 bp · p 0.15 · regional, not allelic
Overall
CADD	22.6	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,341,890). 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.Phe37Cys
Coding: c.110T>G
MANE Select: NM_004826
dbSNP: rs2469653295
Type: single nucleotide variant
Location: chr2:232486544 (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

Similar variants

ECEL1 p.Phe37fs Pathogenic ★★ same residue
ECEL1 p.Arg756Trp Uncertain significance ★★ ⚠ same condition
ECEL1 p.Gly209Val Uncertain significance ★★ ⚠ same condition
ECEL1 p.Pro34Ser Uncertain significance ★★ ⚠ same condition
ECEL1 p.Ser44Arg Uncertain significance ★★ ⚠ same condition
ECEL1 p.Arg355Gln Likely benign ★★ same condition
ECEL1 c.1990-6C>T Conflicting classifications of pathogenicity ★ same condition
ECEL1 p.Ala109Val Uncertain significance ★ ⚠ 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-phe37cys (accessed [today's date]).

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