# NM_001270508.2(TNFAIP3):c.2175G>A (p.Leu725=)

https://sugi.bio/variant/tnfaip3-p-leu725

## Summary

**TNFAIP3 p.Leu725= (c.2175G>A)** is classified **Benign/Likely benign** in TNFAIP3 (ClinVar, Multiple submitters, 9 submitters; last evaluated 2026-04-02). Rare (popmax 0.281%, nfe); Associated with autoinflammatory syndrome, familial, Behcet-like 1.

**At a glance:** Benign/Likely benign · review: Multiple submitters · rsID rs140354477 · 9 submitters · 1 linked condition · rare (popmax 0.281%, nfe)

## For patients & families {#patients}

This is a change in the TNFAIP3 gene that is classified as benign/likely benign — not considered disease-causing, submitted by 9 submitters, and is linked to autoinflammatory syndrome, familial, Behcet-like 1.

*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.*

|  |  |
| --- | --- |
| Diagnostic panels | TNFAIP3 is a diagnostic-grade gene on 3 Genomics England panels |

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0017848/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [TNFAIP3](https://sugi.bio/atlas/gene/TNFAIP3/) |
| Protein change (HGVS p.) | p.Leu725= |
| Coding change (HGVS c.) | c.2175G>A |
| MANE Select transcript | [NM_001270508](https://www.ncbi.nlm.nih.gov/nuccore/NM_001270508) |
| dbSNP | [rs140354477](https://www.ncbi.nlm.nih.gov/snp/rs140354477/) |
| Variant type | single nucleotide variant |
| Location | chr6:137881121-137881121 (GRCh38) |
| ClinVar | [VCV711037](https://www.ncbi.nlm.nih.gov/clinvar/variation/711037/) |

**All HGVS expressions:** `NC_000006.11:g.138202258G>A`, `NC_000006.12:g.137881121G>A`, `NG_032761.1:g.18678G>A`, `NM_001270507.2:c.2175G>A`, `NM_001270508.2:c.2175G>A`, `NM_006290.4:c.2175G>A`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **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 5.128, GERP 1.56, phastCons 1 — highly conserved position (PP3-type support)
- CADD: **PHRED 9.066**. 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** — 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 **0.281%** (nfe) · FAF95 0.273% · FAF99 0.27% · 3,313/1,179,990 in the highest group · 4,183/1,613,870 alleles overall — rare (popmax 0.281%, nfe).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Finnish (not grpmax-eligible) | 0.672% | 149 |
| Ashkenazi Jewish (not grpmax-eligible) | 0.618% | 162 |
| European (non-Finnish) (grpmax) | 0.281% | 356 |
| Remaining individuals (not grpmax-eligible) | 0.219% | 456 |
| Admixed American | 0.115% | 870 |
| African / African-American | 0.0547% | 1,828 |
| Middle Eastern | 0.033% | 3,030 |
| South Asian | 0.00879% | 11,382 |

Finnish 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}

**TNFAIP3** population constraint: LOEUF 0.209, pLI 1, missense-Z 2.6717. *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 **725** lies in the 'interaction with tnip1' region; the 'sufficient for inhibitory activity of tnf-induced nf-kappa-b activity' region; the 'required for lysosomal localization and for traf2 lysosomal degradation' region.

AlphaFold model confidence (whole protein): pLDDT 74.86, 37% of residues very-high.

**17 experimental structure(s)** (PDB): [2EQE](https://www.rcsb.org/structure/2EQE), [2EQF](https://www.rcsb.org/structure/2EQF), [2EQG](https://www.rcsb.org/structure/2EQG), [2VFJ](https://www.rcsb.org/structure/2VFJ), [3DKB](https://www.rcsb.org/structure/3DKB), [3OJ3](https://www.rcsb.org/structure/3OJ3).

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

*Describes the biological roles of TNFAIP3 (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:** TNFAIP3's established molecular role includes protease binding. p.Leu725= falls in the interaction with tnip1 region.


### Pathways affected {#pathways}

TNFAIP3 participates in **6 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [NOD1/2 Signaling Pathway](https://reactome.org/content/detail/R-HSA-168638) | curated |
| [Negative regulators of DDX58/IFIH1 signaling](https://reactome.org/content/detail/R-HSA-936440) | curated |
| [Ovarian tumor domain proteases](https://reactome.org/content/detail/R-HSA-5689896) | curated |
| [Regulation of TNFR1 signaling](https://reactome.org/content/detail/R-HSA-5357905) | curated |
| [TNFR1-induced NF-kappa-B signaling pathway](https://reactome.org/content/detail/R-HSA-5357956) | curated |
| [TNFR1-induced proapoptotic signaling](https://reactome.org/content/detail/R-HSA-5357786) | curated |

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

**Molecular function:** protease binding, ubiquitin-protein transferase activity, cysteine-type deubiquitinase activity, identical protein binding, ubiquitin binding, K63-linked deubiquitinase activity.

**Biological process:** response to molecule of bacterial origin, negative regulation of protein ubiquitination, negative regulation of interleukin-1 beta production, negative regulation of interleukin-2 production, negative regulation of toll-like receptor 3 signaling pathway, protein K11-linked deubiquitination.

## Clinical significance {#significance}

**Benign/Likely benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2026-04-02.

**Submitter consensus:** conflicting (5 Likely benign, 4 Benign).

**Submission history:** 9 submissions (2019–2026); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Genome Diagnostics Laboratory, University Medical Center Utrecht | Likely benign | no assertion criteria provided | clinical testing |  |
| Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Likely benign | no assertion criteria provided | clinical testing |  |
| PreventionGenetics, part of Exact Sciences | Benign | no assertion criteria provided | clinical testing | 2019-07-26 |
| ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Benign | criteria provided, single submitter | clinical testing | 2025-06-25 |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2026-02-01 |
| Mayo Clinic Laboratories, Mayo Clinic | Likely benign | criteria provided, single submitter | clinical testing | 2024-09-04 |
| Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Benign | criteria provided, single submitter | clinical testing | 2026-04-02 |
| CeGaT Center for Human Genetics Tuebingen | Likely benign | criteria provided, single submitter | clinical testing | 2026-02-01 |
| Blueprint Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2024-11-15 |

## Associated conditions {#conditions}

[autoinflammatory syndrome, familial, Behcet-like 1](https://sugi.bio/atlas/disease/autoinflammatory-syndrome-familial-behcet-like-1/).

**Reported phenotype names (ClinVar):** Autoinflammatory syndrome, familial, Behcet-like 1, not provided, TNFAIP3-related disorder, not specified, Haploinsufficiency of A20, AllHighlyPenetrant, TNFAIP3-related condition, none provided.

## Similar variants {#similar}

Related TNFAIP3 variant pages (same residue, condition, or type): [TNFAIP3 p.Arg271Ter](/variant/tnfaip3-p-arg271ter), [TNFAIP3 p.Arg87Ter](/variant/tnfaip3-p-arg87ter), [TNFAIP3 p.Glu366Ter](/variant/tnfaip3-p-glu366ter), [TNFAIP3 p.Ala717Thr](/variant/tnfaip3-p-ala717thr), [TNFAIP3 p.Arg439Gln](/variant/tnfaip3-p-arg439gln), [TNFAIP3 p.Arg569Gln](/variant/tnfaip3-p-arg569gln), [TNFAIP3 p.Arg61Trp](/variant/tnfaip3-p-arg61trp), [TNFAIP3 p.Arg660Lys](/variant/tnfaip3-p-arg660lys).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-06); 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 711037). 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.*