Is CCNP p.Ser30Asn (c.89G>A) pathogenic?

CCNP p.Ser30Asn (c.89G>A) is classified Likely benign in CCNP (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-02-01). AlphaMissense: likely benign (0.1201); Rare (popmax 0.461%, nfe); Associated with CCNP-related disorder.

What condition is associated with CCNP p.Ser30Asn (c.89G>A)?

CCNP p.Ser30Asn (c.89G>A) is associated with CCNP-related disorder (ClinVar).

How common is CCNP p.Ser30Asn (c.89G>A) in the general population?

CCNP p.Ser30Asn (c.89G>A) is rare (popmax 0.461%, nfe) (gnomAD).

What do computational predictors say about CCNP p.Ser30Asn (c.89G>A)?

AlphaMissense predicts likely benign (score 0.1201) — an in-silico prediction, not a clinical call.

CCNP p.Ser30Asn

c.89G>A · rs200091528 · VCV3056810

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1201 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.461%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

CCNP-related disorder

Computational evidence

Protein change
AlphaMissense	0.1201	likely benign
REVEL	0.01	strongly benign-leaning
SaProt	LLR -7.53	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 -0.004	GERP 0.63, phastCons 0.013
Regional constraint	o/e 1.04	unconstrained · MANE · 3,586 bp · p 0.45 · regional, not allelic
Overall
CADD	16.92	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 0.461% European (non-Finnish) · 5,378/1,165,628 alleles

Filtering AF 0.451% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.447%

Overall 0.389% 6,155/1,580,442 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.461%	217
Remaining individualsnot grpmax-eligible	0.408%	245
Middle Eastern	0.403%	248
Ashkenazi Jewishnot grpmax-eligible	0.283%	353
Admixed American	0.261%	382
South Asian	0.238%	420
African / African-American	0.0874%	1,144
Finnishnot grpmax-eligible	0.0199%	5,035
East Asian	0.00228%	43,852

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: CCNP
Protein: p.Ser30Asn
Coding: c.89G>A
MANE Select: NM_024877
dbSNP: rs200091528
Type: single nucleotide variant
Location: chr19:40226553 (GRCh38)
Gene constraint: LOEUF 1.397 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.87

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

Disease context

CCNP-related disorder

Similar variants

CCNP p.Ala142= Likely benign same condition
CCNP p.Ala258= Likely benign same condition
CCNP p.Ala173Ser Uncertain significance ★ ⚠ same type
CCNP p.Ala186Val Uncertain significance ★ ⚠ same type
CCNP p.Ala243Val Uncertain significance ★ ⚠ same type
CCNP p.Ala265Thr Uncertain significance ★ ⚠ same type
CCNP p.Ala37Ser Uncertain significance ★ ⚠ same type
CCNP p.Ala68Glu 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/ccnp-p-ser30asn (accessed [today's date]).

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