# NM_001099402.2(CCNK):c.777A>G (p.Ser259=)

https://sugi.bio/variant/ccnk-p-ser259

## Summary

**CCNK p.Ser259= (c.777A>G)** is classified **Likely benign** in CCNK (ClinVar, Single submitter, 2 submitters; last evaluated 2024-11-20). Ultra-rare (popmax 0.0356%, eas).

**At a glance:** Likely benign · review: Single submitter · rsID rs372835830 · 2 submitters · ultra-rare (popmax 0.0356%, eas)

## For patients & families {#patients}

This is a change in the CCNK gene that is classified as likely benign — not considered disease-causing, submitted by 2 submitters.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

**Support & next steps:** [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [CCNK](https://sugi.bio/atlas/gene/CCNK/) |
| Protein change (HGVS p.) | p.Ser259= |
| Coding change (HGVS c.) | c.777A>G |
| MANE Select transcript | [NM_001144995](https://www.ncbi.nlm.nih.gov/nuccore/NM_001144995) (variant reported on NM_001099402) |
| dbSNP | [rs372835830](https://www.ncbi.nlm.nih.gov/snp/rs372835830/) |
| Variant type | single nucleotide variant |
| Location | chr14:99502750-99502750 (GRCh38) |
| ClinVar | [VCV3035487](https://www.ncbi.nlm.nih.gov/clinvar/variation/3035487/) |

**All HGVS expressions:** `NC_000014.8:g.99969087A>G`, `NC_000014.9:g.99502750A>G`, `NG_130023.1:g.244A>G`, `NM_001099402.2:c.777A>G`, `NM_001144995.2:c.*12496T>C`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP -0.458, GERP -3.08 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 5.103**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- SpliceAI: **not looked up on this page** — it was served without the gene's SpliceAI index, so no lookup was made. This is a gap in this page, not in the data, and says nothing about whether a splicing effect is predicted.
- Population frequency (gnomAD v4.1): grpmax **0.0356%** (eas) · FAF95 0.0223% · FAF99 0.0182% · 16/44,894 in the highest group · 78/1,613,464 alleles overall — ultra-rare (popmax 0.0356%, eas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Remaining individuals (not grpmax-eligible) | 0.0897% | 1,115 |
| East Asian (grpmax) | 0.0356% | 2,806 |
| Admixed American | 0.00333% | 30,001 |
| European (non-Finnish) | 0.000339% | 294,897 |

Remaining individuals shows a higher raw frequency than the grpmax group. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and "Remaining individuals" — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2024-11-20.

**Submitter consensus:** unanimous (2/2 Likely benign).

**Submission history:** 2 submissions (2019–2024); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| PreventionGenetics, part of Exact Sciences | Likely benign | no assertion criteria provided | clinical testing | 2019-03-28 |
| Blueprint Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2024-11-20 |

**Reported phenotype names (ClinVar):** CCNK-related disorder, not specified, CCNK-related condition, AllHighlyPenetrant.

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-11); gnomAD v4.1 (Broad Institute, built 2026-10-06); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-07-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 3035487). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*