Is EMID1 p.Pro330Ser (c.988C>T) pathogenic?

EMID1 p.Pro330Ser (c.988C>T) is classified Uncertain significance in EMID1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-02). Absent from gnomAD v4.1.

How common is EMID1 p.Pro330Ser (c.988C>T) in the general population?

EMID1 p.Pro330Ser (c.988C>T) is absent from gnomAD v4.1 (gnomAD).

EMID1 p.Pro330Ser

c.988C>T · VCV4248642

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,598,184)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.441	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.4	GERP 1.6, phastCons 1
Regional constraint	o/e 0.98	unconstrained · MANE · 53 kb · p 0.62 · regional, not allelic
Overall
CADD	24.3	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,598,184). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: EMID1
Protein: p.Pro330Ser
Coding: c.988C>T
MANE Select: NM_133455
Type: single nucleotide variant
Location: chr22:29234158 (GRCh38)
Gene constraint: LOEUF 0.994 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 51.77
Residue 330: the collagen-like domain; the 'disordered' region

Full EMID1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EMID1 c.587-5C>G Benign ★★ same type
EMID1 p.Ala108Thr Uncertain significance ★ same type
EMID1 p.Ala112Thr Uncertain significance ★ same type
EMID1 p.Ala127Ser Uncertain significance ★ same type
EMID1 p.Ala28Thr Uncertain significance ★ same type
EMID1 p.Ala409Val Uncertain significance ★ same type
EMID1 p.Ala435Asp Uncertain significance ★ same type
EMID1 p.Ala6Ser 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/emid1-p-pro330ser (accessed [today's date]).

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