# NM_139012.3(MAPK14):c.964C>G (p.Pro322Ala)

https://sugi.bio/variant/mapk14-p-pro322ala

## Summary

**MAPK14 p.Pro322Ala (c.964C>G)** is classified **Uncertain significance** in MAPK14 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-18). AlphaMissense: likely benign (0.0746); Ultra-rare (popmax 0.0112%, eas).

**At a glance:** Uncertain significance · review: Single submitter · 1 submitter · AlphaMissense likely benign · ultra-rare (popmax 0.0112%, eas)

## For patients & families {#patients}

This is a change in the MAPK14 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 1 submitter.

*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 | [MAPK14](https://sugi.bio/atlas/gene/MAPK14/) |
| Protein change (HGVS p.) | p.Pro322Ala |
| Coding change (HGVS c.) | c.964C>G |
| MANE Select transcript | [NM_139012](https://www.ncbi.nlm.nih.gov/nuccore/NM_139012) |
| Variant type | single nucleotide variant |
| Location | chr6:36107577-36107577 (GRCh38) |
| ClinVar | [VCV4103753](https://www.ncbi.nlm.nih.gov/clinvar/variation/4103753/) |

**All HGVS expressions:** `NC_000006.11:g.36075354C>G`, `NC_000006.12:g.36107577C>G`, `NM_001315.3:c.964C>G`, `NM_139012.3:c.964C>G`, `NM_139014.3:c.885C>G`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely benign** (0.0746)
- REVEL 0.398 (indeterminate)
- SaProt LLR -8.722 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate
- Conservation: phyloP 7.716, GERP 2.4, phastCons 1 — highly conserved (differs from AlphaMissense)
- CADD: **PHRED 24.3**. 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 0.42** across the covering region of the MANE Select transcript (36,028,244–36,108,444), spanning 80,200 bp. Chi-square p 7.2e-32. 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 **0.0112%** (eas) · FAF95 0.00437% · FAF99 0.00278% · 5/44,542 in the highest group · 6/1,604,550 alleles overall — ultra-rare (popmax 0.0112%, eas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| East Asian (grpmax) | 0.0112% | 8,908 |
| European (non-Finnish) | 8.51e-05% | 1,175,558 |

*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}

**MAPK14** population constraint: LOEUF 0.564, pLI 0.90557, missense-Z 2.9352. *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 **322** lies in a UniProt-annotated variant site (in a lung adenocarcinoma sample; somatic mutation); an α-helix.

AlphaFold model confidence (whole protein): pLDDT 89.91, 75% of residues very-high.

**267 experimental structure(s)** (PDB): [1A9U](https://www.rcsb.org/structure/1A9U), [1BL6](https://www.rcsb.org/structure/1BL6), [1BL7](https://www.rcsb.org/structure/1BL7), [1BMK](https://www.rcsb.org/structure/1BMK), [1DI9](https://www.rcsb.org/structure/1DI9), [1IAN](https://www.rcsb.org/structure/1IAN) — incl. mutant structure 1R3C.

## What this gene does {#gene-function}

*Describes the biological roles of MAPK14 (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** MAPK14's established molecular role includes protein serine/threonine kinase activity. In Reactome, MAPK14 is annotated in disease pathway(s) including **CD163 mediating an anti-inflammatory response**.

**Disease mechanism (Reactome):** MAPK14 loss or alteration is curated in [CD163 mediating an anti-inflammatory response](https://reactome.org/content/detail/R-HSA-9662834).

### Pathways affected {#pathways}

MAPK14 participates in **18 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [CD163 mediating an anti-inflammatory response](https://reactome.org/content/detail/R-HSA-9662834) | other |
| [ADP signalling through P2Y purinoceptor 1](https://reactome.org/content/detail/R-HSA-418592) | other |
| [Activation of PPARGC1A (PGC-1alpha) by phosphorylation](https://reactome.org/content/detail/R-HSA-2151209) | other |
| [Activation of the AP-1 family of transcription factors](https://reactome.org/content/detail/R-HSA-450341) | other |
| [ERK/MAPK targets](https://reactome.org/content/detail/R-HSA-198753) | other |
| [KSRP (KHSRP) binds and destabilizes mRNA](https://reactome.org/content/detail/R-HSA-450604) | other |
| [Myogenesis](https://reactome.org/content/detail/R-HSA-525793) | other |
| [NOD1/2 Signaling Pathway](https://reactome.org/content/detail/R-HSA-168638) | other |
| [Neutrophil degranulation](https://reactome.org/content/detail/R-HSA-6798695) | other |
| [Oxidative Stress Induced Senescence](https://reactome.org/content/detail/R-HSA-2559580) | other |
| [Platelet sensitization by LDL](https://reactome.org/content/detail/R-HSA-432142) | other |
| [RHO GTPases Activate NADPH Oxidases](https://reactome.org/content/detail/R-HSA-5668599) | other |
| [Regulation of MITF-M-dependent genes involved in pigmentation](https://reactome.org/content/detail/R-HSA-9824585) | other |
| [Regulation of TP53 Activity through Phosphorylation](https://reactome.org/content/detail/R-HSA-6804756) | other |
| [Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A](https://reactome.org/content/detail/R-HSA-69601) | other |
| [VEGFA-VEGFR2 Pathway](https://reactome.org/content/detail/R-HSA-4420097) | other |
| [activated TAK1 mediates p38 MAPK activation](https://reactome.org/content/detail/R-HSA-450302) | other |
| [p38MAPK events](https://reactome.org/content/detail/R-HSA-171007) | other |

### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** protein serine/threonine kinase activity, MAP kinase activity, enzyme binding, protein phosphatase binding, mitogen-activated protein kinase p38 binding.

**Biological process:** positive regulation of gene expression, stress-activated protein kinase signaling cascade, positive regulation of cyclase activity, positive regulation of interleukin-12 production, negative regulation of hippo signaling, intracellular signal transduction.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2025-06-18.

**Submitter consensus:** unanimous (1/1 Uncertain significance).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Ambry Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2025-06-18 |

**Reported phenotype names (ClinVar):** not specified, AllHighlyPenetrant.

## Similar variants {#similar}

Related MAPK14 variant pages (same residue, condition, or type): [MAPK14 p.Pro322Thr](/variant/mapk14-p-pro322thr), [MAPK14 c.763-2308A>G](/variant/mapk14-c-763-minus-2308a-g), [MAPK14 c.763-2312A>G](/variant/mapk14-c-763-minus-2312a-g), [MAPK14 c.763-2316G>A](/variant/mapk14-c-763-minus-2316g-a), [MAPK14 c.763-2341C>G](/variant/mapk14-c-763-minus-2341c-g), [MAPK14 c.763-2356G>A](/variant/mapk14-c-763-minus-2356g-a), [MAPK14 p.Ala304Val](/variant/mapk14-p-ala304val), [MAPK14 p.Ala41Thr](/variant/mapk14-p-ala41thr).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-14); 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 2026-10-14); 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 4103753). 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.*