Is CAMKK2 p.Phe267= (c.801C>T) pathogenic?

CAMKK2 p.Phe267= (c.801C>T) is classified Likely benign in CAMKK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-29). Ultra-rare (popmax 0.0192%, nfe).

How common is CAMKK2 p.Phe267= (c.801C>T) in the general population?

CAMKK2 p.Phe267= (c.801C>T) is ultra-rare (popmax 0.0192%, nfe) (gnomAD).

CAMKK2 p.Phe267=

c.801C>T · rs201031410 · VCV3136823

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0192%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.36 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.67	GERP -2.9, phastCons 0.94
Overall
CADD	7.917	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0192% European (non-Finnish) · 226/1,179,856 alleles

Filtering AF 0.0171% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0162%

Overall 0.0147% 238/1,613,708 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0192%	5,221
Remaining individualsnot grpmax-eligible	0.0064%	15,620
Admixed American	0.005%	19,986
African / African-American	0.00401%	24,956
East Asian	0.00223%	44,888
South Asian	0.0011%	91,070

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: CAMKK2
Protein: p.Phe267=
Coding: c.801C>T
MANE Select: NM_001270485
dbSNP: rs201031410
Type: single nucleotide variant
Location: chr12:121255800 (GRCh38)
Gene constraint: LOEUF 0.649 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.93 · 24 PDB
Residue 267: the protein kinase domain; a β-strand

Full CAMKK2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CAMKK2 c.1235+3G>A Benign ★★ same type
CAMKK2 p.Asn118= Benign ★★ same type
CAMKK2 p.Gly22= Benign ★★ same type
CAMKK2 p.His150= Benign ★★ same type
CAMKK2 p.Ile297= Benign ★★ same type
CAMKK2 p.Pro351= Benign ★★ same type
CAMKK2 p.Ser133= Benign ★★ same type
CAMKK2 p.Ala15Val 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/camkk2-p-phe267 (accessed [today's date]).

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