# NM_001354712.2(THRB):c.1354C>T (p.Pro452Ser)

https://sugi.bio/variant/thrb-p-pro452ser

## Summary

**THRB p.Pro452Ser (c.1354C>T)** is classified **Conflicting classifications of pathogenicity** in THRB (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2026-03-04). AlphaMissense: likely pathogenic (0.9891); Absent from gnomAD v4.1; Associated with THRB-related disorder.

**At a glance:** Conflicting classifications of pathogenicity · review: Conflicting submitters · rsID rs2148780678 · 4 submitters · 2 linked conditions · AlphaMissense likely pathogenic · absent from gnomAD v4.1

## For patients & families {#patients}

This is a change in the THRB gene that is of uncertain or conflicting significance (submitters disagree on it), submitted by 4 submitters, and is linked to THRB-related disorder.

*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 | [THRB](https://sugi.bio/atlas/gene/THRB/) |
| Protein change (HGVS p.) | p.Pro452Ser |
| Coding change (HGVS c.) | c.1354C>T |
| MANE Select transcript | [NM_001354712](https://www.ncbi.nlm.nih.gov/nuccore/NM_001354712) |
| dbSNP | [rs2148780678](https://www.ncbi.nlm.nih.gov/snp/rs2148780678/) |
| Variant type | single nucleotide variant |
| Location | chr3:24122916-24122916 (GRCh38) |
| ClinVar | [VCV1705477](https://www.ncbi.nlm.nih.gov/clinvar/variation/1705477/) |

**All HGVS expressions:** `NC_000003.11:g.24164407G>A`, `NC_000003.12:g.24122916G>A`, `NG_009159.1:g.376907C>T`, `NM_000461.4:c.1354C>T`, `NM_000461.5:c.1354C>T`, `NM_001128176.3:c.1354C>T`, `NM_001128177.2:c.1354C>T`, `NM_001252634.2:c.1354C>T`, `NM_001354708.2:c.1354C>T`, `NM_001354709.2:c.1354C>T`, `NM_001354710.2:c.1354C>T`, `NM_001354711.2:c.1354C>T`, `NM_001354712.2:c.1354C>T`, `NM_001354713.2:c.1354C>T`, `NM_001354714.2:c.1261C>T`, `NM_001354715.2:c.1261C>T`, `NM_001374822.1:c.1354C>T`, `NM_001374823.1:c.1354C>T`, `NM_001374824.1:c.1354C>T`, `NM_001374825.1:c.1354C>T`, `NM_001374826.1:c.1354C>T`, `NM_001374827.1:c.1183C>T`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely pathogenic** (0.9891)
- REVEL 0.86 (moderately pathogenic-leaning) — agrees with AlphaMissense
- SaProt LLR -9.461 (tolerated) — differs from AlphaMissense
- → **In-silico consensus:** AlphaMissense and REVEL call this damaging; SaProt does not
- Conservation: phyloP 11.931, GERP 2.06, phastCons 1 — highly conserved (agrees)
- CADD: **PHRED 28.8**. 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 0.15** across the covering region of the MANE Select transcript (24,122,887–24,122,990), spanning 103 bp — the region is depleted of missense variation. Chi-square p 5.9e-09. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code 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: **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}

**THRB** population constraint: LOEUF 0.43, pLI 0.9992, missense-Z 3.7158. *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 **452** lies in the nr lbd domain; the 'interaction with nr2f6' region.

AlphaFold model confidence (whole protein): pLDDT 80.24, 69% of residues very-high.

**34 experimental structure(s)** (PDB): [1BSX](https://www.rcsb.org/structure/1BSX), [1N46](https://www.rcsb.org/structure/1N46), [1NAX](https://www.rcsb.org/structure/1NAX), [1NQ0](https://www.rcsb.org/structure/1NQ0), [1NQ1](https://www.rcsb.org/structure/1NQ1), [1NQ2](https://www.rcsb.org/structure/1NQ2) — incl. mutant structure 1NQ2.

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

*Describes the biological roles of THRB (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:** THRB's established molecular role includes transcription coactivator binding. p.Pro452Ser falls in the nr lbd domain.


### Pathways affected {#pathways}

THRB participates in **2 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Nuclear Receptor transcription pathway](https://reactome.org/content/detail/R-HSA-383280) | curated |
| [SUMOylation of intracellular receptors](https://reactome.org/content/detail/R-HSA-4090294) | curated |

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

**Molecular function:** transcription coactivator binding, nuclear receptor activity, enzyme binding, thyroid hormone binding, sequence-specific double-stranded DNA binding.

**Biological process:** positive regulation of thyroid hormone receptor signaling pathway, mRNA transcription by RNA polymerase II, positive regulation of transcription by RNA polymerase II, cellular response to thyroid hormone stimulus.

## Clinical significance {#significance}

**Conflicting classifications of pathogenicity** — review status Conflicting submitters *(criteria provided, conflicting classifications)*, last evaluated 2026-03-04.

**Submitter consensus:** conflicting (2 Likely pathogenic, 2 Uncertain significance).

**Submission history:** 4 submissions (2022–2026); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| 3billion | Likely pathogenic | criteria provided, single submitter | clinical testing | 2022-09-01 |
| Quest Diagnostics Nichols Institute San Juan Capistrano | Uncertain significance | criteria provided, single submitter | clinical testing | 2025-03-18 |
| Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2026-03-04 |
| Blueprint Genetics | Likely pathogenic | criteria provided, single submitter | clinical testing | 2023-06-06 |

## Associated conditions {#conditions}

[THRB-related disorder](https://sugi.bio/atlas/disease/thrb-related-disorder/), [thyroid hormone resistance, generalized, autosomal dominant](https://sugi.bio/atlas/disease/thyroid-hormone-resistance-generalized-autosomal-dominant/).

**Reported phenotype names (ClinVar):** THRB-related disorder, Thyroid hormone resistance, generalized, autosomal dominant, not specified, not provided, THRB-related condition, none provided, AllHighlyPenetrant, HYPERTHYROXINEMIA, FAMILIAL EUTHYROID, SECONDARY TO PITUITARY AND PERIPHERAL RESISTANCE TO THYROID HORMONES.

## Similar variants {#similar}

Related THRB variant pages (same residue, condition, or type): [THRB p.Pro452Thr](/variant/thrb-p-pro452thr), [THRB p.Pro452Arg](/variant/thrb-p-pro452arg), [THRB p.Pro452=](/variant/thrb-p-pro452), [THRB p.Ala268Gly](/variant/thrb-p-ala268gly), [THRB p.Ala317Thr](/variant/thrb-p-ala317thr), [THRB p.Arg316His](/variant/thrb-p-arg316his), [THRB p.Arg320Cys](/variant/thrb-p-arg320cys), [THRB p.Arg320His](/variant/thrb-p-arg320his).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-11); 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 2026-07-14); 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 1705477). 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.*