Is ELP2 p.Pro4Ala (c.10C>G) pathogenic?

ELP2 p.Pro4Ala (c.10C>G) is classified Uncertain significance in ELP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-17). AlphaMissense: likely benign (0.0573); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with ELP2 p.Pro4Ala (c.10C>G)?

ELP2 p.Pro4Ala (c.10C>G) is associated with Inborn genetic diseases (ClinVar).

How common is ELP2 p.Pro4Ala (c.10C>G) in the general population?

ELP2 p.Pro4Ala (c.10C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ELP2 p.Pro4Ala (c.10C>G)?

AlphaMissense predicts likely benign (score 0.0573) — an in-silico prediction, not a clinical call.

ELP2 p.Pro4Ala

c.10C>G · rs770664170 · VCV3088497

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0573 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0573	likely benign
REVEL	0.03	moderately benign-leaning
SaProt	LLR -6.81	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1	GERP -4.3
Regional constraint	o/e 0.95	unconstrained · MANE · 45 kb · p 0.13 · regional, not allelic
Overall
CADD	13.85	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.Pro4Ala
Coding: c.10C>G
MANE Select: NM_018255
dbSNP: rs770664170
Type: single nucleotide variant
Location: chr18:36129943 (GRCh38)
Gene constraint: LOEUF 0.869 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.49 · 4 PDB

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-pro4ala (accessed [today's date]).

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