# NM_001199867.2(MARK4):c.1609C>G (p.Pro537Ala)

https://sugi.bio/variant/mark4-p-pro537ala

## Summary

**MARK4 p.Pro537Ala (c.1609C>G)** is classified **Uncertain significance** in MARK4 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-14). AlphaMissense: likely benign (0.0485); Very rare (popmax 0.000524%, nfe).

**At a glance:** Uncertain significance · review: Single submitter · 1 submitter · AlphaMissense likely benign · very rare (popmax 0.000524%, nfe)

## For patients & families {#patients}

This is a change in the MARK4 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 | [MARK4](https://sugi.bio/atlas/gene/MARK4/) |
| Protein change (HGVS p.) | p.Pro537Ala |
| Coding change (HGVS c.) | c.1609C>G |
| MANE Select transcript | [NM_001199867](https://www.ncbi.nlm.nih.gov/nuccore/NM_001199867) |
| Variant type | single nucleotide variant |
| Location | chr19:45297686-45297686 (GRCh38) |
| ClinVar | [VCV4104161](https://www.ncbi.nlm.nih.gov/clinvar/variation/4104161/) |

**All HGVS expressions:** `NC_000019.10:g.45297686C>G`, `NC_000019.9:g.45800944C>G`, `NM_001199867.2:c.1609C>G`, `NM_031417.4:c.1609C>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** (0.0485)
- REVEL 0.034 (moderately benign-leaning) — agrees with AlphaMissense
- SaProt LLR -7.008 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- Conservation: phyloP 1.351, GERP -3.27, phastCons 1 — weakly conserved position
- CADD: **PHRED 15.43**. 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 0.88** across the covering region of the MANE Select transcript (45,278,583–45,302,707), spanning 24,124 bp. Chi-square p 0.0023. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **below the reporting threshold**. This position is scored for a different substitution (C>T, Δ0.26 acceptor gain), so this allele was evaluated and its deltas all fell under Δ0.2 — a prediction of no splicing effect for this allele, not a gap in our data. *No ACMG code assigned.*
- Population frequency (gnomAD v4.1): grpmax **0.000524%** (nfe) · FAF95 0.000188% · FAF99 0.000124% · 6/1,145,292 in the highest group · 7/1,527,752 alleles overall — very rare (popmax 0.000524%, nfe).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Remaining individuals (not grpmax-eligible) | 0.0017% | 58,780 |
| European (non-Finnish) (grpmax) | 0.000524% | 190,882 |

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.*

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

**MARK4** population constraint: LOEUF 0.361, pLI 1, missense-Z 2.9454. *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 **537** lies in the 'disordered' region.

AlphaFold model confidence (whole protein): pLDDT 67.97, 38% of residues very-high.

**2 experimental structure(s)** (PDB): [5ES1](https://www.rcsb.org/structure/5ES1), [8XFL](https://www.rcsb.org/structure/8XFL).

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

*Describes the biological roles of MARK4 (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:** MARK4's established molecular role includes protein serine/threonine kinase activity. p.Pro537Ala falls in the disordered region.


### Pathways affected {#pathways}

MARK4 participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Anchoring of the basal body to the plasma membrane](https://reactome.org/content/detail/R-HSA-5620912) | curated |

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

**Molecular function:** protein serine/threonine kinase activity, microtubule binding, cytoskeletal adaptor activity, gamma-tubulin binding, tau-protein kinase activity.

**Biological process:** microtubule cytoskeleton organization, microtubule bundle formation, protein phosphorylation, nervous system development, cilium organization, positive regulation of cilium assembly.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2025-08-14.

**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 | 2025-08-14 |

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

## Similar variants {#similar}

Related MARK4 variant pages (same residue, condition, or type): [MARK4 p.Leu226=](/variant/mark4-p-leu226), [MARK4 p.Thr461=](/variant/mark4-p-thr461), [MARK4 p.Ala168Ser](/variant/mark4-p-ala168ser), [MARK4 p.Ala389Val](/variant/mark4-p-ala389val), [MARK4 p.Ala457Val](/variant/mark4-p-ala457val), [MARK4 p.Ala462Val](/variant/mark4-p-ala462val), [MARK4 p.Ala479Thr](/variant/mark4-p-ala479thr), [MARK4 p.Ala47Thr](/variant/mark4-p-ala47thr).

### 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 4104161). 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.*