Is CENPF p.Glu1982fs (c.5943del) pathogenic?

CENPF p.Glu1982fs (c.5943del) is classified Likely pathogenic in CENPF (ClinVar, Single submitter, 1 submitter; last evaluated 2018-04-23). Very rare (popmax 0.00401%, afr).

How common is CENPF p.Glu1982fs (c.5943del) in the general population?

CENPF p.Glu1982fs (c.5943del) is very rare (popmax 0.00401%, afr) (gnomAD).

CENPF p.Glu1982fs

c.5943del · rs779235200 · VCV524136

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00401%, afr)

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 13 of 20
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.4	GERP 2, phastCons 0.88
Overall
CADD	25.2	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00401% African / African-American · 3/74,884 alleles

Filtering AF 0.00106% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000495%

Overall 0.000186% 3/1,613,910 alleles · very rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CENPF
Protein: p.Glu1982fs
Coding: c.5943del
MANE Select: NM_016343
dbSNP: rs779235200
Type: Deletion
Location: chr1:214645513 (GRCh38)
Gene constraint: LOEUF 0.734 · pLI <0.01 (gnomAD)

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

Similar variants

CENPF p.Asp1397fs Likely pathogenic ★★ same type
CENPF p.Glu342fs Pathogenic/Likely pathogenic ★★ same type
CENPF p.Ala1515fs Likely pathogenic ★ same type
CENPF p.Ala699_Tyr700insTer Likely pathogenic ★ same type
CENPF p.Arg3014fs Likely pathogenic ★ same type
CENPF p.Asn57fs Pathogenic ★ same type
CENPF p.Glu1172fs Pathogenic ★ same type
CENPF p.Glu251fs Likely 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/cenpf-p-glu1982fs (accessed [today's date]).

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