# NM_021138.4(TRAF2):c.547C>T (p.Pro183Ser)

https://sugi.bio/variant/traf2-p-pro183ser

## Summary

**TRAF2 p.Pro183Ser (c.547C>T)** is classified **Uncertain significance** in TRAF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-28). AlphaMissense: likely benign (0.1934); Ultra-rare (popmax 0.0164%, mid).

**At a glance:** Uncertain significance · review: Single submitter · rsID rs750248731 · 1 submitter · AlphaMissense likely benign · ultra-rare (popmax 0.0164%, mid)

## For patients & families {#patients}

This is a change in the TRAF2 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 | [TRAF2](https://sugi.bio/atlas/gene/TRAF2/) |
| Protein change (HGVS p.) | p.Pro183Ser |
| Coding change (HGVS c.) | c.547C>T |
| MANE Select transcript | [NM_021138](https://www.ncbi.nlm.nih.gov/nuccore/NM_021138) |
| dbSNP | [rs750248731](https://www.ncbi.nlm.nih.gov/snp/rs750248731/) |
| Variant type | single nucleotide variant |
| Location | chr9:136909938-136909938 (GRCh38) |
| ClinVar | [VCV2491654](https://www.ncbi.nlm.nih.gov/clinvar/variation/2491654/) |

**All HGVS expressions:** `NC_000009.11:g.139804390C>T`, `NC_000009.12:g.136909938C>T`, `NM_021138.4:c.547C>T`, `NM_145718.1:c.703C>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** (0.1934)
- REVEL 0.193 (benign-leaning) — agrees with AlphaMissense
- SaProt LLR -9.383 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- Conservation: phyloP 4.671, GERP 1.18, phastCons 1 — highly conserved (differs from AlphaMissense)
- CADD: **PHRED 24.8**. 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: **not assessed** — this absence is genuinely unknown. Where a position sits between the lowest and the highest record the release holds for its gene, an absent score is a result and we state it as one; this position falls outside them, or the gene has no scored position at all, so that test did not reach here. It may lie outside the scored MANE transcript scope, or it may have been scored with all four deltas below Δ0.2 just past the last surviving record. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **0.0164%** (mid) · FAF95 0.00359% · FAF99 0.00255% · 1/6,084 in the highest group · 15/1,614,066 alleles overall — ultra-rare (popmax 0.0164%, mid).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Middle Eastern (grpmax) | 0.0164% | 6,084 |
| South Asian | 0.00769% | 13,011 |
| Remaining individuals (not grpmax-eligible) | 0.0016% | 62,488 |
| African / African-American | 0.00133% | 74,928 |
| European (non-Finnish) | 0.000424% | 236,009 |

*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.*

## Protein context {#protein}

Residue **183** lies in the 'necessary for interaction with traf6' region; the 'traf family member interaction' region.

AlphaFold model confidence (whole protein): pLDDT 60.31, 22% of residues very-high.

**3 experimental structure(s)** (PDB): [1KZZ](https://www.rcsb.org/structure/1KZZ), [1L0A](https://www.rcsb.org/structure/1L0A), [5H10](https://www.rcsb.org/structure/5H10).

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

*Describes the biological roles of TRAF2 (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:** TRAF2's established molecular role includes ubiquitin protein ligase binding. p.Pro183Ser falls in the necessary for interaction with traf6 region.


### Pathways affected {#pathways}

TRAF2 participates in **5 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE)](https://reactome.org/content/detail/R-HSA-936964) | curated |
| [Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 ](https://reactome.org/content/detail/R-HSA-9824878) | curated |
| [Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation](https://reactome.org/content/detail/R-HSA-9828211) | curated |
| [TICAM1-dependent activation of IRF3/IRF7](https://reactome.org/content/detail/R-HSA-9013973) | curated |
| [TRAF6 mediated IRF7 activation](https://reactome.org/content/detail/R-HSA-933541) | curated |

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

**Molecular function:** ubiquitin protein ligase binding, deubiquitinase activator activity, identical protein binding, molecular adaptor activity.

**Biological process:** DNA damage response, positive regulation of type I interferon production, negative regulation of canonical NF-kappaB signal transduction, cellular response to interleukin-1, cellular response to tumor necrosis factor, cellular response to ionizing radiation.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2023-02-28.

**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 | 2023-02-28 |

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

## Similar variants {#similar}

Related TRAF2 variant pages (same residue, condition, or type): [TANK p.Gln113Glu](/variant/tank-p-gln113glu), [TRAF2 p.Arg308=](/variant/traf2-p-arg308), [TRAF2 p.Gly81=](/variant/traf2-p-gly81), [TRAF2 p.Phe361=](/variant/traf2-p-phe361), [TANK p.Arg40Ser](/variant/tank-p-arg40ser), [TANK p.Arg42Cys](/variant/tank-p-arg42cys), [TANK p.Asn87Ser](/variant/tank-p-asn87ser), [TANK p.Asn88Ile](/variant/tank-p-asn88ile).

### 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 2491654). 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.*