Is EMC1 p.Val564fs (c.1691del) pathogenic?

EMC1 p.Val564fs (c.1691del) is classified Pathogenic in EMC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-17). Associated with cerebellar atrophy, visual impairment, and psychomotor retardation;.

What condition is associated with EMC1 p.Val564fs (c.1691del)?

EMC1 p.Val564fs (c.1691del) is associated with cerebellar atrophy, visual impairment, and psychomotor retardation; (ClinVar).

EMC1 p.Val564fs

c.1691del · VCV3375420

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

cerebellar atrophy, visual impairment, and psychomotor retardation;

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 15 of 23
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.5	GERP -4.3, phastCons 0.99

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

Variant & gene context

Gene: EMC1
Protein: p.Val564fs
Coding: c.1691del
MANE Select: NM_015047
Type: Deletion
Location: chr1:19232715 (GRCh38)
Gene constraint: LOEUF 0.913 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.67 · 10 PDB

Full EMC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

cerebellar atrophy, visual impairment, and psychomotor retardation; — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EMC1 p.Asn739fs Pathogenic/Likely pathogenic ★★ same condition
EMC1 p.Pro874fs Pathogenic/Likely pathogenic ★★ same condition
EMC1 c.2675_2676del Pathogenic/Likely pathogenic ★★ same condition
EMC1 c.287-1G>A Likely pathogenic ★★ same condition
EMC1 c.787-1G>A Likely pathogenic ★★ same condition
EMC1 p.Arg660Ter Pathogenic/Likely pathogenic ★★ same condition
EMC1 p.Arg69Ter Pathogenic/Likely pathogenic ★★ same condition
EMC1 p.Leu266Ter Pathogenic/Likely pathogenic ★★ 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/emc1-p-val564fs (accessed [today's date]).

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