Is IER3IP1 p.Ser50= (c.150A>G) pathogenic?

IER3IP1 p.Ser50= (c.150A>G) is classified Likely benign in IER3IP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-24). Absent from gnomAD v4.1; Associated with microcephaly, epilepsy, and diabetes syndrome.

What condition is associated with IER3IP1 p.Ser50= (c.150A>G)?

IER3IP1 p.Ser50= (c.150A>G) is associated with microcephaly, epilepsy, and diabetes syndrome (ClinVar).

How common is IER3IP1 p.Ser50= (c.150A>G) in the general population?

IER3IP1 p.Ser50= (c.150A>G) is absent from gnomAD v4.1 (gnomAD).

IER3IP1 p.Ser50=

c.150A>G · rs1599992528 · VCV796805

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

microcephaly, epilepsy, and diabetes syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.58	GERP -3.1, phastCons 0.91
Overall
CADD	5.808	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: IER3IP1
Protein: p.Ser50=
Coding: c.150A>G
MANE Select: NM_016097
dbSNP: rs1599992528
Type: single nucleotide variant
Location: chr18:47157479 (GRCh38)
Gene constraint: LOEUF 1.905 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.57

Full IER3IP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

microcephaly, epilepsy, and diabetes syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

IER3IP1 p.Ser50Leu Uncertain significance ★ ⚠ same residue
IER3IP1 p.Leu78Pro Pathogenic/Likely pathogenic ★★ ⚠ same condition
IER3IP1 p.Ala74Gly Uncertain significance ★★ ⚠ same condition
IER3IP1 p.Arg57Leu Uncertain significance ★★ ⚠ same condition
IER3IP1 p.Asn54Lys Uncertain significance ★★ ⚠ same condition
IER3IP1 p.Gln10His Uncertain significance ★★ ⚠ same condition
IER3IP1 p.Gly40Cys Uncertain significance ★★ ⚠ same condition
IER3IP1 p.Ile73Thr 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/ier3ip1-p-ser50 (accessed [today's date]).

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