Is CEP164 p.Glu649fs (c.1946del) pathogenic?

CEP164 p.Glu649fs (c.1946del) is classified Pathogenic in CEP164 (ClinVar, Single submitter, 1 submitter; last evaluated 2016-03-03). Absent from gnomAD.

How common is CEP164 p.Glu649fs (c.1946del) in the general population?

CEP164 p.Glu649fs (c.1946del) is absent from gnomAD (gnomAD).

CEP164 p.Glu649fs

c.1946del · rs886041567 · VCV280343

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 16 of 33
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.5	GERP 1.4, phastCons 1

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: CEP164
Protein: p.Glu649fs
Coding: c.1946del
MANE Select: NM_014956
dbSNP: rs886041567
Type: Deletion
Location: chr11:117390788 (GRCh38)
Gene constraint: LOEUF 1.009 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.08 · 4 PDB

Full CEP164 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEP164 p.Glu649= Likely benign ★ same residue
CEP164 p.Arg897fs Pathogenic/Likely pathogenic ★★ same type
CEP164 p.Glu704fs Pathogenic/Likely pathogenic ★★ same type
CEP164 p.Glu745fs Likely pathogenic ★★ same type
CEP164 p.Leu433fs Pathogenic/Likely pathogenic ★★ same type
CEP164 p.Trp1336fs Pathogenic/Likely pathogenic ★★ same type
CEP164 c.3278+5_3278+8del Uncertain significance ★★ same type
CEP164 p.Glu745del 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/cep164-p-glu649fs (accessed [today's date]).

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