# NM_001377265.1(MAPT):c.2091T>C (p.Ser697=)

https://sugi.bio/variant/mapt-p-ser697

## Summary

**MAPT p.Ser697= (c.2091T>C)** is classified **Pathogenic/Likely pathogenic** in MAPT (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-02-24). Absent from gnomAD v4.1; Associated with frontotemporal dementia.

**At a glance:** Pathogenic/Likely pathogenic · review: Multiple submitters · rsID rs63750568 · 3 submitters · 1 linked condition · absent from gnomAD v4.1

## For patients & families {#patients}

This is a change in the MAPT gene that is considered likely disease-causing, submitted by 3 submitters, and is linked to frontotemporal dementia.

*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.*

|  |  |
| --- | --- |
| Clinical trials | 146 registered for this condition — see ClinicalTrials.gov |

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0008436/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [MAPT](https://sugi.bio/atlas/gene/MAPT/) |
| Protein change (HGVS p.) | p.Ser697= |
| Coding change (HGVS c.) | c.2091T>C |
| MANE Select transcript | [NM_001377265](https://www.ncbi.nlm.nih.gov/nuccore/NM_001377265) |
| dbSNP | [rs63750568](https://www.ncbi.nlm.nih.gov/snp/rs63750568/) |
| Variant type | single nucleotide variant |
| Location | chr17:46010402-46010402 (GRCh38) |
| ClinVar | [VCV98217](https://www.ncbi.nlm.nih.gov/clinvar/variation/98217/) |

**All HGVS expressions:** `LRG_660:g.120940T>C`, `LRG_660t1:c.1866T>C`, `LRG_660t2:c.2091T>C`, `NC_000017.10:g.44087768T>C`, `NC_000017.11:g.46010402T>C`, `NG_007398.2:g.120940T>C`, `NM_001123066.4:c.1920T>C`, `NM_001123067.4:c.828T>C`, `NM_001203251.2:c.736-3841T>C`, `NM_001203252.2:c.823-3841T>C`, `NM_001377265.1:c.2091T>C`, `NM_001377266.1:c.1801-3841T>C`, `NM_001377267.1:c.736-3841T>C`, `NM_001377268.1:c.649-3841T>C`, `NM_005910.6:c.915T>C`, `NM_016834.5:c.741T>C`, `NM_016835.5:c.1866T>C`, `NM_016841.5:c.649-3841T>C`

## Computational & population evidence {#evidence}

**Concordance:** 1 independent predictor **concordant** with the ClinVar classification.

- **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 4.962, GERP 5.84, phastCons 1 — highly conserved position (PP3-type support)
- CADD: **PHRED 17.03**. 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: **no splice effect predicted**. SpliceAI outputs four numbers per variant, not one: acceptor loss, donor loss, acceptor gain, donor gain (DS_AL / DS_DL / DS_AG / DS_DG). The release publishes its own filter rule, which we read from the dataset rather than assume: an allele is reported only if the largest of its four deltas reaches 0.2. This allele is not in the release, so all four of its deltas are under 0.2. No figure is shown because none was read: the bound is deduced from that absence. It is a result, not a gap in our data, and here that is proven rather than inferred: a different substitution at this very position, T>G, IS in the release and scores Δ0.31 donor gain, so SpliceAI evaluated this position and this allele was not among the ones that cleared the filter. *ClinGen's SVI treats the largest of the four as evidence against a splicing effect at or below 0.1, where it may support BP4, and as uninformative between 0.1 and 0.2. We cannot tell which applies here, so these SpliceAI data support neither BP4 nor PP3; that is a statement about this evidence alone, not about the variant's other evidence.*
- Population frequency: **absent from gnomAD v4.1** — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

*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}

**MAPT** population constraint: LOEUF 0.723, pLI 2.1814e-05, missense-Z 2.4904; ClinGen dosage — haploinsufficiency 0/3, triplosensitivity 0/3. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 49.56, 0% of residues very-high.

**299 experimental structure(s)** (PDB): [10IJ](https://www.rcsb.org/structure/10IJ), [10IK](https://www.rcsb.org/structure/10IK), [1I8H](https://www.rcsb.org/structure/1I8H), [22JY](https://www.rcsb.org/structure/22JY), [28LJ](https://www.rcsb.org/structure/28LJ), [28LO](https://www.rcsb.org/structure/28LO) — incl. mutant structure 6GK7.

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

*Describes the biological roles of MAPT (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:** MAPT's established molecular role includes enzyme inhibitor activity.


### Pathways affected {#pathways}

MAPT participates in **3 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Caspase-mediated cleavage of cytoskeletal proteins](https://reactome.org/content/detail/R-HSA-264870) | curated |
| [Activation of AMPK downstream of NMDARs](https://reactome.org/content/detail/R-HSA-9619483) | other |
| [PKR-mediated signaling](https://reactome.org/content/detail/R-HSA-9833482) | other |

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

**Molecular function:** enzyme inhibitor activity, microtubule binding, SH3 domain binding, enzyme binding, protein kinase binding, apolipoprotein binding.

**Biological process:** microtubule cytoskeleton organization, DNA damage response, synapse assembly, learning or memory, memory, regulation of autophagy.

## Clinical significance {#significance}

**Pathogenic/Likely pathogenic** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2024-02-24.

**Submitter consensus:** conflicting (1 not provided, 1 Pathogenic, 1 Likely pathogenic).

**Submission history:** 3 submissions (2019–2024); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| VIB  Department of Molecular Genetics, University of Antwerp | not provided | no classification provided | not provided |  |
| Mendelics | Pathogenic | criteria provided, single submitter | clinical testing | 2019-05-28 |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely pathogenic | criteria provided, single submitter | clinical testing | 2024-02-24 |

## Associated conditions {#conditions}

[frontotemporal dementia](https://sugi.bio/atlas/disease/frontotemporal-dementia/).

**Reported phenotype names (ClinVar):** Frontotemporal dementia, not provided, none provided, Frontotemporal Dementia with Parkinsonism-17 (FTDP-17), FRONTOTEMPORAL DEMENTIA WITH PARKINSONISM, FRONTOTEMPORAL LOBE DEMENTIA, MULTIPLE SYSTEM TAUOPATHY WITH PRESENILE DEMENTIA, Dementia, frontotemporal, with or without parkinsonism, WILHELMSEN-LYNCH DISEASE, Frontotemporal lobe dementia (FLDEM).

## Same-residue context {#hotspot}

Residue **697** carries **1 other pathogenic ClinVar variant** — a recurrently-mutated position: [MAPT p.Ser697Asn](/variant/mapt-p-ser697asn). *Positional co-occurrence of independent ClinVar records, not functional proof.*

## Similar variants {#similar}

Related MAPT variant pages (same residue, condition, or type): [MAPT p.Ser697Asn](/variant/mapt-p-ser697asn), [MAPT p.Ser697Ile](/variant/mapt-p-ser697ile), [MAPT c.1999-10G>T](/variant/mapt-c-1999-minus-10g-t), [MAPT c.2091+16C>T](/variant/mapt-c-2091-plus-16c-t), [MAPT c.2091+3G>A](/variant/mapt-c-2091-plus-3g-a), [MAPT p.Arg798Trp](/variant/mapt-p-arg798trp), [MAPT p.Asn671Lys](/variant/mapt-p-asn671lys), [MAPT p.Asn688=](/variant/mapt-p-asn688).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-15); 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 98217). 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.*