Is EGLN1 p.Ala172= (c.516G>T) pathogenic?

EGLN1 p.Ala172= (c.516G>T) is classified Likely benign in EGLN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-31). Absent from gnomAD v4.1.

How common is EGLN1 p.Ala172= (c.516G>T) in the general population?

EGLN1 p.Ala172= (c.516G>T) is absent from gnomAD v4.1 (gnomAD).

EGLN1 p.Ala172=

c.516G>T · rs755769412 · VCV2626710

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.26	GERP -3.4, phastCons 0.78
Overall
CADD	7.361	PHRED · no single calibrated threshold — expert panels disagree

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: EGLN1
Protein: p.Ala172=
Coding: c.516G>T
MANE Select: NM_022051
dbSNP: rs755769412
Type: single nucleotide variant
Location: chr1:231421373 (GRCh38)
Gene constraint: LOEUF 0.739 · pLI 0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.81 · 67 PDB
Residue 172: the 'disordered' region

Full EGLN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EGLN1 p.Ala172Ser Uncertain significance ★ ⚠ same residue
EGLN1 p.Ala172Thr Uncertain significance ★ ⚠ same residue
EGLN1 p.Ala172Val Conflicting classifications of pathogenicity ★ ⚠ same residue
EGLN1 p.Ala172Gly Likely benign ★ same residue
EGLN1 c.1216+6C>T Uncertain significance ★★ same type
EGLN1 p.Ala103Val Uncertain significance ★★ ⚠ same type
EGLN1 p.Ala114Thr Uncertain significance ★★ ⚠ same type
EGLN1 p.Ala121Gly 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/egln1-p-ala172 (accessed [today's date]).

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