# NM_000535.7(PMS2):c.1210C>T (p.Pro404Ser)

https://sugi.bio/variant/pms2-p-pro404ser

## Summary

**PMS2 p.Pro404Ser (c.1210C>T)** is classified **Uncertain significance** in PMS2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2023-11-02). AlphaMissense: likely benign (0.069); Absent from gnomAD v4.1; Associated with Lynch syndrome.

**At a glance:** Uncertain significance · review: Multiple submitters · rsID rs2128736131 · 3 submitters · 2 linked conditions · AlphaMissense likely benign · absent from gnomAD v4.1

## For patients & families {#patients}

This is a change in the PMS2 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 3 submitters, and is linked to Lynch syndrome.

*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.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal dominant |
| Age of onset (of this condition) | Adult |
| Clinical trials | 106 registered for this condition — see ClinicalTrials.gov |
| Diagnostic panels | PMS2 is a diagnostic-grade gene on 23 Genomics England panels |

**Commonly reported features of Lynch syndrome** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Weight loss — Very frequent (99-80%)
- Constipation — Very frequent (99-80%)
- Malabsorption — Very frequent (99-80%)
- Abdominal pain — Very frequent (99-80%)
- Gastrointestinal hemorrhage — Very frequent (99-80%)
- Neoplasm of the skin — Very frequent (99-80%)
- Adenoma sebaceum — Very frequent (99-80%)
- Glioblastoma multiforme — Very frequent (99-80%)

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

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [PMS2](https://sugi.bio/atlas/gene/PMS2/) |
| Protein change (HGVS p.) | p.Pro404Ser |
| Coding change (HGVS c.) | c.1210C>T |
| MANE Select transcript | [NM_000535](https://www.ncbi.nlm.nih.gov/nuccore/NM_000535) |
| dbSNP | [rs2128736131](https://www.ncbi.nlm.nih.gov/snp/rs2128736131/) |
| Variant type | single nucleotide variant |
| Location | chr7:5987555-5987555 (GRCh38) |
| ClinVar | [VCV1750304](https://www.ncbi.nlm.nih.gov/clinvar/variation/1750304/) |

**All HGVS expressions:** `LRG_161:g.26552C>T`, `LRG_161t1:c.1210C>T`, `NC_000007.13:g.6027186G>A`, `NC_000007.14:g.5987555G>A`, `NG_008466.1:g.26552C>T`, `NM_000535.7:c.1210C>T`, `NM_001018040.1:c.805C>T`, `NM_001322003.2:c.805C>T`, `NM_001322004.2:c.805C>T`, `NM_001322005.2:c.805C>T`, `NM_001322006.2:c.1054C>T`, `NM_001322007.2:c.892C>T`, `NM_001322008.2:c.892C>T`, `NM_001322009.2:c.805C>T`, `NM_001322010.2:c.649C>T`, `NM_001322011.2:c.277C>T`, `NM_001322012.2:c.277C>T`, `NM_001322013.2:c.637C>T`, `NM_001322014.2:c.1210C>T`, `NM_001322015.2:c.901C>T`, `NM_001406866.1:c.1396C>T`, `NM_001406868.1:c.1234C>T`, `NM_001406869.1:c.1102C>T`, `NM_001406870.1:c.1054C>T`, `NM_001406871.1:c.1210C>T`, `NM_001406872.1:c.1210C>T`, `NM_001406873.1:c.1012C>T`, `NM_001406874.1:c.1042C>T`, `NM_001406875.1:c.901C>T`, `NM_001406876.1:c.892C>T`, `NM_001406877.1:c.901C>T`, `NM_001406878.1:c.901C>T`, `NM_001406879.1:c.901C>T`, `NM_001406880.1:c.901C>T`, `NM_001406881.1:c.901C>T`, `NM_001406882.1:c.901C>T`, `NM_001406883.1:c.892C>T`, `NM_001406884.1:c.886C>T`, `NM_001406885.1:c.874C>T`, `NM_001406886.1:c.844C>T`, `NM_001406887.1:c.805C>T`, `NM_001406888.1:c.805C>T`, `NM_001406889.1:c.805C>T`, `NM_001406890.1:c.805C>T`, `NM_001406891.1:c.805C>T`, `NM_001406892.1:c.805C>T`, `NM_001406893.1:c.805C>T`, `NM_001406894.1:c.805C>T`, `NM_001406895.1:c.805C>T`, `NM_001406896.1:c.805C>T`, `NM_001406897.1:c.805C>T`, `NM_001406898.1:c.805C>T`, `NM_001406899.1:c.805C>T`, `NM_001406900.1:c.745C>T`, `NM_001406901.1:c.736C>T`, `NM_001406902.1:c.736C>T`, `NM_001406903.1:c.892C>T`, `NM_001406904.1:c.697C>T`, `NM_001406905.1:c.697C>T`, `NM_001406906.1:c.649C>T`, `NM_001406907.1:c.649C>T`, `NM_001406908.1:c.805C>T`, `NM_001406909.1:c.637C>T`, `NM_001406910.1:c.805C>T`, `NM_001406911.1:c.439C>T`, `NR_003085.2:n.1292C>T`, `NR_136154.1:n.1297C>T`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely benign** (0.069)
- REVEL 0.11 (moderately benign-leaning) — agrees with AlphaMissense
- SaProt LLR -5.077 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- Conservation: phyloP -1.643 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 1.749**. 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 1.09** across the covering region of the MANE Select transcript (5,986,798–6,009,019), spanning 22,221 bp. Chi-square p 0.015. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code 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). A loss score is an existing splice site weakened or destroyed; a gain score is a new site created or an existing one strengthened. 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. No allele at this position is in the release, so all four are under 0.2 for every alternate allele here. 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, because the release scores every possible substitution across the transcripts it covers (Ensembl MANE v1.4) before it filters, so what survives for a gene is one continuous stretch. What is measured is that this position sits inside the stretch covered for PMS2 (1,053 scored positions, the nearest 8 bases away); what is taken from the release's own description, rather than measured, is that coverage inside that stretch is continuous. On that, SpliceAI did score it. *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}

**PMS2** population constraint: LOEUF 0.898, pLI 5.3905e-09, missense-Z 0.36886; ClinGen dosage — haploinsufficiency 3/3, triplosensitivity 0/3. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **Lynch syndrome** — Definitive (AD)
- **hereditary breast carcinoma** — Disputed (AD)
- **mismatch repair cancer syndrome 1** — Definitive (AR)

## Protein context {#protein}

Residue **404** lies in the 'disordered' region.

AlphaFold model confidence (whole protein): pLDDT 71.37, 36% of residues very-high.

**9 experimental structure(s)** (PDB): [1EA6](https://www.rcsb.org/structure/1EA6), [1H7S](https://www.rcsb.org/structure/1H7S), [1H7U](https://www.rcsb.org/structure/1H7U), [5U5R](https://www.rcsb.org/structure/5U5R), [6MFQ](https://www.rcsb.org/structure/6MFQ), [7RCB](https://www.rcsb.org/structure/7RCB) — incl. mutant structure 6MFQ.

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

*Describes the biological roles of PMS2 (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:** PMS2's established molecular role includes DNA binding. p.Pro404Ser falls in the disordered region. In Reactome, PMS2 is annotated in disease pathway(s) including **Defective Mismatch Repair Associated With MLH1**, **Defective Mismatch Repair Associated With PMS2**.

**Disease mechanism (Reactome):** PMS2 loss or alteration is curated in [Defective Mismatch Repair Associated With MLH1](https://reactome.org/content/detail/R-HSA-5545483), [Defective Mismatch Repair Associated With PMS2](https://reactome.org/content/detail/R-HSA-5632987).

### Pathways affected {#pathways}

PMS2 participates in **6 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Defective Mismatch Repair Associated With MLH1](https://reactome.org/content/detail/R-HSA-5545483) | curated |
| ⚕ [Defective Mismatch Repair Associated With PMS2](https://reactome.org/content/detail/R-HSA-5632987) | curated |
| [Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha)](https://reactome.org/content/detail/R-HSA-5358565) | curated |
| [Somatic hypermutation of immunoglobulin genes by error-prone mismatch repair (MMR)](https://reactome.org/content/detail/R-HSA-9968295) | curated |
| [TP53 Regulates Transcription of DNA Repair Genes](https://reactome.org/content/detail/R-HSA-6796648) | curated |
| [Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta)](https://reactome.org/content/detail/R-HSA-5358606) | electronic |

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

**Molecular function:** DNA binding, single base insertion or deletion binding.

**Biological process:** meiotic mismatch repair, mismatch repair.

## Clinical significance {#significance}

**Uncertain significance** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2023-11-02.

**Submitter consensus:** conflicting (2 Uncertain significance, 1 Uncertain Significance).

**Submission history:** 3 submissions (2018–2023); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| All of Us Research Program, National Institutes of Health | Uncertain Significance | criteria provided, single submitter | clinical testing | 2023-11-02 |
| Ambry Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2018-06-19 |
| Labcorp Genetics (formerly Invitae), Labcorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2023-08-17 |

## Associated conditions {#conditions}

[Lynch syndrome](https://sugi.bio/atlas/disease/lynch-syndrome/), [hereditary neoplastic syndrome](https://sugi.bio/atlas/disease/hereditary-neoplastic-syndrome/).

**Reported phenotype names (ClinVar):** Lynch syndrome, Hereditary cancer-predisposing syndrome, Hereditary nonpolyposis colorectal neoplasms, Hereditary Cancer Syndrome, Hereditary neoplastic syndrome, Neoplastic Syndromes, Hereditary, Tumor predisposition.

## Same-residue context {#hotspot}

Residue **404** carries **1 other pathogenic ClinVar variant** — a recurrently-mutated position: [PMS2 p.Pro404fs](/variant/pms2-p-pro404fs). *Positional co-occurrence of independent ClinVar records, not functional proof.*

## Similar variants {#similar}

Related PMS2 variant pages (same residue, condition, or type): [PMS2 p.Pro404Leu](/variant/pms2-p-pro404leu), [PMS2 p.Pro404=](/variant/pms2-p-pro404), [PMS2 p.Pro404Arg](/variant/pms2-p-pro404arg), [PMS2 c.1144+2T>A](/variant/pms2-c-1144-plus-2t-a), [PMS2 c.163+2T>C](/variant/pms2-c-163-plus-2t-c), [PMS2 c.164-2A>G](/variant/pms2-c-164-minus-2a-g), [PMS2 c.2007-1G>A](/variant/pms2-c-2007-minus-1g-a), [PMS2 c.2174+1G>A](/variant/pms2-c-2174-plus-1g-a).

### 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 1750304). 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.*