Is CER1 p.Ile230Val (c.688A>G) pathogenic?

CER1 p.Ile230Val (c.688A>G) is classified Likely benign in CER1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-20). AlphaMissense: likely benign (0.0682); Ultra-rare (popmax 0.016%, afr).

How common is CER1 p.Ile230Val (c.688A>G) in the general population?

CER1 p.Ile230Val (c.688A>G) is ultra-rare (popmax 0.016%, afr) (gnomAD).

What do computational predictors say about CER1 p.Ile230Val (c.688A>G)?

AlphaMissense predicts likely benign (score 0.0682) — an in-silico prediction, not a clinical call.

CER1 p.Ile230Val

c.688A>G · VCV3490993

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0682 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.016%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0682	likely benign
REVEL	0.034	moderately benign-leaning
SaProt	LLR -6.19	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · T>A here scores Δ0.31 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.62	GERP -1.2, phastCons 0.99
Regional constraint	o/e 1.32	unconstrained · MANE · 2,579 bp · p 8.8e-09 · regional, not allelic
Overall
CADD	3.556	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 0.016% African / African-American · 12/74,900 alleles

Filtering AF 0.00922% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00722%

Overall 0.000867% 14/1,614,048 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.016%	6,242
Admixed American	0.00333%	30,002

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: CER1
Protein: p.Ile230Val
Coding: c.688A>G
Type: single nucleotide variant
Location: chr9:14720206 (GRCh38)

Full CER1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CER1 p.Ala198Val Uncertain significance ★ ⚠ same type
CER1 p.Ala199Gly Uncertain significance ★ ⚠ same type
CER1 p.Ala199Val Uncertain significance ★ ⚠ same type
CER1 p.Ala59Thr Uncertain significance ★ ⚠ same type
CER1 p.Arg24Cys Uncertain significance ★ ⚠ same type
CER1 p.Arg24His Uncertain significance ★ ⚠ same type
CER1 p.Arg85Lys Uncertain significance ★ ⚠ same type
CER1 p.Arg92Thr 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/cer1-p-ile230val (accessed [today's date]).

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