Is ELP2 p.Ser809Thr (c.2426G>C) pathogenic?

ELP2 p.Ser809Thr (c.2426G>C) is classified Uncertain significance in ELP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-30). AlphaMissense: likely benign (0.1344); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with ELP2 p.Ser809Thr (c.2426G>C)?

ELP2 p.Ser809Thr (c.2426G>C) is associated with Inborn genetic diseases (ClinVar).

How common is ELP2 p.Ser809Thr (c.2426G>C) in the general population?

ELP2 p.Ser809Thr (c.2426G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ELP2 p.Ser809Thr (c.2426G>C)?

AlphaMissense predicts likely benign (score 0.1344) — an in-silico prediction, not a clinical call.

ELP2 p.Ser809Thr

c.2426G>C · rs2511364655 · VCV2614718

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1344 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1344	likely benign
REVEL	0.491	indeterminate
SaProt	LLR -7.98	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.6, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 45 kb · p 0.13 · regional, not allelic
Overall
CADD	25.8	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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: ELP2
Protein: p.Ser809Thr
Coding: c.2426G>C
MANE Select: NM_018255
dbSNP: rs2511364655
Type: single nucleotide variant
Location: chr18:36174586 (GRCh38)
Gene constraint: LOEUF 0.869 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.49 · 4 PDB
Residue 809: a β-strand

Full ELP2 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

ELP2 p.Ala741Val Uncertain significance ★★ ⚠ same condition
ELP2 p.Arg468Trp Uncertain significance ★★ ⚠ same condition
ELP2 p.Asp71Gly Uncertain significance ★★ ⚠ same condition
ELP2 p.Gln606Pro Uncertain significance ★★ ⚠ same condition
ELP2 p.Val728Ile Uncertain significance ★★ ⚠ same condition
ELP2 p.Asn709Ser Likely benign ★★ same condition
ELP2 p.Glu263Gly Likely benign ★★ ⚠ same condition
ELP2 p.Tyr439Cys Likely benign ★★ 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/elp2-p-ser809thr (accessed [today's date]).

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