Is EQTN p.Ser239Pro (c.715T>C) pathogenic?

EQTN p.Ser239Pro (c.715T>C) is classified Uncertain significance in EQTN (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-22). AlphaMissense: likely pathogenic (0.8777); Absent from gnomAD v4.1.

How common is EQTN p.Ser239Pro (c.715T>C) in the general population?

EQTN p.Ser239Pro (c.715T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EQTN p.Ser239Pro (c.715T>C)?

AlphaMissense predicts likely pathogenic (score 0.8777) — an in-silico prediction, not a clinical call.

EQTN p.Ser239Pro

c.715T>C · VCV4250357

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8777 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8777	likely pathogenic · top 4% in EQTN
REVEL	0.245	benign-leaning
SaProt	LLR -7.23	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.9	GERP 1.7, phastCons 1
Regional constraint	o/e 1.13	unconstrained · MANE · 12 kb · p 0.016 · regional, not allelic
Overall
CADD	26.1	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: EQTN
Protein: p.Ser239Pro
Coding: c.715T>C
MANE Select: NM_020641
Type: single nucleotide variant
Location: chr9:27284893 (GRCh38)
Gene constraint: LOEUF 1.732 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 59.20

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

Similar variants

EQTN p.Ala146Gly Uncertain significance ★ ⚠ same type
EQTN p.Ala146Ser Uncertain significance ★ ⚠ same type
EQTN p.Ala247Val Uncertain significance ★ ⚠ same type
EQTN p.Ala93Val Uncertain significance ★ ⚠ same type
EQTN p.Arg126Ser Uncertain significance ★ ⚠ same type
EQTN p.Arg294Gln Uncertain significance ★ ⚠ same type
EQTN p.Arg85Ser Uncertain significance ★ ⚠ same type
EQTN p.Asn288Lys Uncertain significance ★ ⚠ same type

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/eqtn-p-ser239pro (accessed [today's date]).

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