# NM_003260.5(TLE2):c.422G>A (p.Arg141His)

https://sugi.bio/variant/tle2-p-arg141his

## Summary

**TLE2 p.Arg141His (c.422G>A)** is classified **Uncertain significance** in TLE2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-18). AlphaMissense: likely benign (0.0687); Ultra-rare (popmax 0.0487%, eas).

**At a glance:** Uncertain significance · review: Single submitter · rsID rs576245434 · 1 submitter · AlphaMissense likely benign · ultra-rare (popmax 0.0487%, eas)

## For patients & families {#patients}

This is a change in the TLE2 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 | [TLE2](https://sugi.bio/atlas/gene/TLE2/) |
| Protein change (HGVS p.) | p.Arg141His |
| Coding change (HGVS c.) | c.422G>A |
| MANE Select transcript | [NM_003260](https://www.ncbi.nlm.nih.gov/nuccore/NM_003260) |
| dbSNP | [rs576245434](https://www.ncbi.nlm.nih.gov/snp/rs576245434/) |
| Variant type | single nucleotide variant |
| Location | chr19:3019411-3019411 (GRCh38) |
| ClinVar | [VCV3177814](https://www.ncbi.nlm.nih.gov/clinvar/variation/3177814/) |

**All HGVS expressions:** `NC_000019.10:g.3019411C>T`, `NC_000019.9:g.3019409C>T`, `NM_001144761.2:c.464G>A`, `NM_001144762.2:c.204+288G>A`, `NM_001300846.2:c.425G>A`, `NM_003260.5:c.422G>A`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely benign** (0.0687)
- REVEL 0.053 (moderately benign-leaning) — agrees with AlphaMissense
- SaProt LLR -3.64 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- Conservation: phyloP 5.547, phastCons 1 — highly conserved (differs from AlphaMissense)
- CADD: **PHRED 22.8**. 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.*
- Regional missense constraint: **o/e 1.03** across the covering region of the MANE Select transcript (2,997,851–3,028,904), spanning 31,053 bp. Chi-square p 0.36. 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). 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, C>G, IS in the release and scores Δ0.21 acceptor 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 (gnomAD v4.1): grpmax **0.0487%** (eas) · FAF95 0.0322% · FAF99 0.027% · 20/41,096 in the highest group · 29/1,538,372 alleles overall — ultra-rare (popmax 0.0487%, eas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| East Asian (grpmax) | 0.0487% | 2,055 |
| Remaining individuals (not grpmax-eligible) | 0.00333% | 30,009 |
| African / African-American | 0.00137% | 73,244 |
| South Asian | 0.00119% | 84,054 |
| European (non-Finnish) | 0.000436% | 229,543 |

*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}

**TLE2** population constraint: LOEUF 1.02, pLI 1.8431e-21, missense-Z -0.83722. *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 **141** lies in the 'gp domain' region.

AlphaFold model confidence (whole protein): pLDDT 68.40, 41% of residues very-high.

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

*Describes the biological roles of TLE2 (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:** TLE2's established molecular role includes transcription corepressor activity. p.Arg141His falls in the gp domain region.


### Pathways affected {#pathways}

TLE2 participates in **4 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Deactivation of the beta-catenin transactivating complex](https://reactome.org/content/detail/R-HSA-3769402) | curated |
| [Formation of the beta-catenin:TCF transactivating complex](https://reactome.org/content/detail/R-HSA-201722) | curated |
| [NOTCH1 Intracellular Domain Regulates Transcription](https://reactome.org/content/detail/R-HSA-2122947) | electronic |
| [Repression of WNT target genes](https://reactome.org/content/detail/R-HSA-4641265) | electronic |

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

**Molecular function:** transcription corepressor activity.

**Biological process:** negative regulation of DNA-templated transcription, negative regulation of canonical Wnt signaling pathway.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2023-11-18.

**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 | 2023-11-18 |

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

## Similar variants {#similar}

Related TLE2 variant pages (same residue, condition, or type): [TLE2 p.Ala110Thr](/variant/tle2-p-ala110thr), [TLE2 p.Ala133Val](/variant/tle2-p-ala133val), [TLE2 p.Ala164Val](/variant/tle2-p-ala164val), [TLE2 p.Ala167Val](/variant/tle2-p-ala167val), [TLE2 p.Ala168Val](/variant/tle2-p-ala168val), [TLE2 p.Ala187Ser](/variant/tle2-p-ala187ser), [TLE2 p.Ala187Val](/variant/tle2-p-ala187val), [TLE2 p.Ala192Val](/variant/tle2-p-ala192val).

### 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 3177814). 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.*