# NM_152515.5(CKAP2L):c.789A>T (p.Arg263Ser)

https://sugi.bio/variant/ckap2l-p-arg263ser

## Summary

**CKAP2L p.Arg263Ser (c.789A>T)** is classified **Benign** in CKAP2L (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-02-01). AlphaMissense: likely benign (0.2067); Common (popmax 18.1%, afr) — too common for a highly-penetrant pathogenic allele.

**At a glance:** Benign · review: Multiple submitters · rsID rs17042341 · 3 submitters · AlphaMissense likely benign · common (popmax 18.1%, afr) — too common for a highly-penetrant pathogenic allele

## For patients & families {#patients}

This is a change in the CKAP2L gene that is classified as benign — not considered disease-causing, submitted by 3 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 | [CKAP2L](https://sugi.bio/atlas/gene/CKAP2L/) |
| Protein change (HGVS p.) | p.Arg263Ser |
| Coding change (HGVS c.) | c.789A>T |
| MANE Select transcript | [NM_152515](https://www.ncbi.nlm.nih.gov/nuccore/NM_152515) |
| dbSNP | [rs17042341](https://www.ncbi.nlm.nih.gov/snp/rs17042341/) |
| Variant type | single nucleotide variant |
| Location | chr2:112756582-112756582 (GRCh38) |
| ClinVar | [VCV1175564](https://www.ncbi.nlm.nih.gov/clinvar/variation/1175564/) |

**All HGVS expressions:** `NC_000002.11:g.113514159T>A`, `NC_000002.12:g.112756582T>A`, `NG_041820.1:g.13096A>T`, `NM_001304361.2:c.294A>T`, `NM_152515.5:c.789A>T`

## Computational & population evidence {#evidence}

**Concordance:** Evidence sources **disagree** — common (popmax 18.1%, afr) — too common for a highly-penetrant pathogenic allele.

- AlphaMissense **likely benign** (0.2067)
- REVEL 0.03 (moderately benign-leaning) — agrees with AlphaMissense
- SaProt LLR -5.913 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- Conservation: phyloP 0.25, GERP -0.956 — weakly conserved position
- CADD: **PHRED 14.38**. 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.*
- Regional missense constraint: **o/e 1.04** across the covering region of the MANE Select transcript (112,738,826–112,764,598), spanning 25,772 bp. Chi-square p 0.21. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **18.1%** (afr) · FAF95 17.9% · FAF99 17.7% · 13,542/74,788 in the highest group · 84,074/1,612,376 alleles overall — common (popmax 18.1%, afr) — too common for a highly-penetrant pathogenic allele.

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| African / African-American (grpmax) | 18.1% | 6 |
| Remaining individuals (not grpmax-eligible) | 5.44% | 18 |
| European (non-Finnish) | 5.08% | 20 |
| Middle Eastern | 5.04% | 20 |
| Admixed American | 3.95% | 25 |
| Ashkenazi Jewish (not grpmax-eligible) | 3.77% | 27 |
| South Asian | 2.26% | 44 |
| Finnish (not grpmax-eligible) | 2.11% | 47 |
| Amish (not grpmax-eligible) | 0.33% | 303 |
| East Asian | 0.0111% | 8,977 |

*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.*

## Gene constraint & dosage {#gene-context}

**CKAP2L** population constraint: LOEUF 0.72, pLI 0.00013949, missense-Z -0.018164. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}

Residue **263** lies in a UniProt-annotated variant site (in); the 'disordered' region.

AlphaFold model confidence (whole protein): pLDDT 54.68, 8% of residues very-high.

## Clinical significance {#significance}

**Benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2026-02-01.

**Submitter consensus:** unanimous (3/3 Benign).

**Submission history:** 3 submissions (2021–2026); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| GeneDx | Benign | criteria provided, single submitter | clinical testing | 2021-06-09 |
| Breakthrough Genomics, Breakthrough Genomics | Benign | criteria provided, single submitter | not provided |  |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2026-02-01 |

**Reported phenotype names (ClinVar):** not provided, none provided.

## Similar variants {#similar}

Related CKAP2L variant pages (same residue, condition, or type): [CKAP2L p.Arg206Gly](/variant/ckap2l-p-arg206gly), [CKAP2L p.Arg284Trp](/variant/ckap2l-p-arg284trp), [CKAP2L p.Arg347Lys](/variant/ckap2l-p-arg347lys), [CKAP2L p.Arg688Gln](/variant/ckap2l-p-arg688gln), [CKAP2L p.Cys725Ser](/variant/ckap2l-p-cys725ser), [CKAP2L p.Gln428Arg](/variant/ckap2l-p-gln428arg), [CKAP2L p.Glu462Val](/variant/ckap2l-p-glu462val), [CKAP2L p.Ile283Leu](/variant/ckap2l-p-ile283leu).

### 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 1175564). 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.*