Is CEP120 p.Ala40Ser (c.118G>T) pathogenic?

CEP120 p.Ala40Ser (c.118G>T) is classified Uncertain significance in CEP120 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-05-04). AlphaMissense: likely benign (0.1011); Ultra-rare (popmax 0.0254%, afr); Associated with Inborn genetic diseases.

What condition is associated with CEP120 p.Ala40Ser (c.118G>T)?

CEP120 p.Ala40Ser (c.118G>T) is associated with Inborn genetic diseases (ClinVar).

How common is CEP120 p.Ala40Ser (c.118G>T) in the general population?

CEP120 p.Ala40Ser (c.118G>T) is ultra-rare (popmax 0.0254%, afr) (gnomAD).

What do computational predictors say about CEP120 p.Ala40Ser (c.118G>T)?

AlphaMissense predicts likely benign (score 0.1011) — an in-silico prediction, not a clinical call.

CEP120 p.Ala40Ser

c.118G>T · rs779768191 · VCV2387567

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1011 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0254%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1011	likely benign
REVEL	0.107	moderately benign-leaning
SaProt	LLR -4.66	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 0.93, phastCons 1
Regional constraint	o/e 1.06	unconstrained · MANE · 76 kb · p 0.029 · regional, not allelic
Overall
CADD	21.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0254% African / African-American · 19/74,890 alleles

Filtering AF 0.0166% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0137%

Overall 0.00118% 19/1,612,368 alleles · ultra-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: CEP120
Protein: p.Ala40Ser
Coding: c.118G>T
MANE Select: NM_001375405
dbSNP: rs779768191
Type: single nucleotide variant
Location: chr5:123418447 (GRCh38)
Gene constraint: LOEUF 0.93 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.22 · 4 PDB
Residue 40: the c2 1 domain; a β-strand

Full CEP120 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CEP120 p.Arg611Cys Uncertain significance ★★ ⚠ same condition
CEP120 p.Arg611Leu Uncertain significance ★★ ⚠ same condition
CEP120 p.Arg722Gln Uncertain significance ★★ ⚠ same condition
CEP120 p.Arg722Pro Uncertain significance ★★ ⚠ same condition
CEP120 p.Arg746Gln Uncertain significance ★★ ⚠ same condition
CEP120 p.Arg904Ile Uncertain significance ★★ ⚠ same condition
CEP120 p.Asn242His Uncertain significance ★★ ⚠ same condition
CEP120 p.Asn435Ser Uncertain significance ★★ ⚠ 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/cep120-p-ala40ser (accessed [today's date]).

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