Is CEP152 p.Phe5Ser (c.14T>C) pathogenic?

CEP152 p.Phe5Ser (c.14T>C) is classified Uncertain significance in CEP152 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-12). AlphaMissense: likely pathogenic (0.6007); Very rare (popmax 0.00167%, amr).

How common is CEP152 p.Phe5Ser (c.14T>C) in the general population?

CEP152 p.Phe5Ser (c.14T>C) is very rare (popmax 0.00167%, amr) (gnomAD).

What do computational predictors say about CEP152 p.Phe5Ser (c.14T>C)?

AlphaMissense predicts likely pathogenic (score 0.6007) — an in-silico prediction, not a clinical call.

CEP152 p.Phe5Ser

c.14T>C · rs1380569944 · VCV2962411

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6007 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.6007	likely pathogenic · top 10% in CEP152
REVEL	0.738	pathogenic-leaning
SaProt	LLR -5.17	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 4.9, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 67 kb · p 0.21 · regional, not allelic
Overall
CADD	25.7	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/59,964 alleles

Filtering AF 7.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.4e-05%

Overall 0.00031% 5/1,613,368 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	59,964
European (non-Finnish)	0.000339%	294,955

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: CEP152
Protein: p.Phe5Ser
Coding: c.14T>C
MANE Select: NM_001194998
dbSNP: rs1380569944
Type: single nucleotide variant
Location: chr15:48805636 (GRCh38)
Gene constraint: LOEUF 0.784 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.54 · 3 PDB
Residue 5: the 'interaction with plk4' region; the 'disordered' region

Full CEP152 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEP152 p.Phe5= Likely benign ★ same residue
CEP152 c.1578-1G>A Likely pathogenic ★★ same type
CEP152 c.1908+1G>T Likely pathogenic ★★ same type
CEP152 c.540+1G>A Pathogenic/Likely pathogenic ★★ same type
CEP152 c.88-2A>G Likely pathogenic ★★ same type
CEP152 c.972+2T>A Likely pathogenic ★★ same type
CEP152 p.Arg115Ter Pathogenic/Likely pathogenic ★★ same type
CEP152 p.Arg1309Ter Pathogenic/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/cep152-p-phe5ser (accessed [today's date]).

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