Is EMD p.Thr43Ser (c.128C>G) pathogenic?

EMD p.Thr43Ser (c.128C>G) is classified Uncertain significance in EMD (ClinVar, Single submitter, 1 submitter; last evaluated 2018-03-15). AlphaMissense: likely benign (0.1613); Absent from gnomAD v4.1.

How common is EMD p.Thr43Ser (c.128C>G) in the general population?

EMD p.Thr43Ser (c.128C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EMD p.Thr43Ser (c.128C>G)?

AlphaMissense predicts likely benign (score 0.1613) — an in-silico prediction, not a clinical call.

EMD p.Thr43Ser

c.128C>G · rs1569552081 · VCV618081

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1613 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1613	likely benign
REVEL	0.028	moderately benign-leaning
SaProt	LLR -5.90	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 3.7	GERP -1.4, phastCons 1
Regional constraint	o/e 1.05	unconstrained · MANE · 1,709 bp · p 0.47 · regional, not allelic
Overall
CADD	16.76	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: EMD
Protein: p.Thr43Ser
Coding: c.128C>G
MANE Select: NM_000117
dbSNP: rs1569552081
Type: single nucleotide variant
Location: chrX:154379735 (GRCh38)
Structure: AlphaFold pLDDT 61.26 · 6 PDB
Residue 43: the lem domain; an α-helix

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

Similar variants

EMD p.Thr43Ile Uncertain significance ★ ⚠ same residue
EMD p.Thr43= Likely benign ★ same residue
EMD c.187+1G>A Pathogenic ★★ same type
EMD c.187+1G>T Pathogenic/Likely pathogenic ★★ same type
EMD c.265+1G>A Likely pathogenic ★★ same type
EMD c.265+2T>A Likely pathogenic ★★ same type
EMD c.266-2A>G Pathogenic ★★ same type
EMD c.266-3A>G Pathogenic ★★ 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/emd-p-thr43ser (accessed [today's date]).

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