Is EMC10 p.Ser23fs (c.66del) pathogenic?

EMC10 p.Ser23fs (c.66del) is classified Pathogenic in EMC10 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-09-06). No gnomAD frequency available for this variant; Associated with neurodevelopmental disorder with dysmorphic facies and variable seizures.

What condition is associated with EMC10 p.Ser23fs (c.66del)?

EMC10 p.Ser23fs (c.66del) is associated with neurodevelopmental disorder with dysmorphic facies and variable seizures (ClinVar).

How common is EMC10 p.Ser23fs (c.66del) in the general population?

EMC10 p.Ser23fs (c.66del) is no gnomAD frequency available for this variant (gnomAD).

EMC10 p.Ser23fs

c.66del · rs2513789400 · VCV1704220

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

neurodevelopmental disorder with dysmorphic facies and variable seizures

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -2.2	GERP -2.4

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: EMC10
Protein: p.Ser23fs
Coding: c.66del
MANE Select: NM_001308429 · reported on NM_206538
dbSNP: rs2513789400
Type: Deletion
Location: chr19:50476608 (GRCh38)

Full EMC10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

neurodevelopmental disorder with dysmorphic facies and variable seizures — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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/emc10-p-ser23fs (accessed [today's date]).

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