# NM_152468.5(TMC8):c.1209G>A (p.Lys403=)

https://sugi.bio/variant/tmc8-p-lys403

## Summary

**TMC8 p.Lys403= (c.1209G>A)** is classified **Benign** in TMC8 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-27). Low-frequency (popmax 1.85%, afr); Associated with epidermodysplasia verruciformis.

**At a glance:** Benign · review: Multiple submitters · rsID rs76467743 · 3 submitters · 1 linked condition · low-frequency (popmax 1.85%, afr)

## For patients & families {#patients}

This is a change in the TMC8 gene that is classified as benign — not considered disease-causing, submitted by 3 submitters, and is linked to epidermodysplasia verruciformis.

*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 recessive |
| Age of onset (of this condition) | All ages |
| Clinical trials | 1 registered for this condition — see ClinicalTrials.gov |
| Diagnostic panels | TMC8 is a diagnostic-grade gene on 4 Genomics England panels |

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

- Seborrheic dermatitis — Very frequent (99-80%)
- Recurrent skin infections — Very frequent (99-80%)
- Abnormality of the immune system — Very frequent (99-80%)
- Papule — Very frequent (99-80%)
- Skin plaque — Very frequent (99-80%)
- Pustule — Very frequent (99-80%)
- Verrucae — Very frequent (99-80%)
- Hypopigmented skin patches — Frequent (79-30%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0006357/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [TMC8](https://sugi.bio/atlas/gene/TMC8/) |
| Protein change (HGVS p.) | p.Lys403= |
| Coding change (HGVS c.) | c.1209G>A |
| MANE Select transcript | [NM_152468](https://www.ncbi.nlm.nih.gov/nuccore/NM_152468) |
| dbSNP | [rs76467743](https://www.ncbi.nlm.nih.gov/snp/rs76467743/) |
| Variant type | single nucleotide variant |
| Location | chr17:78137316-78137316 (GRCh38) |
| ClinVar | [VCV526246](https://www.ncbi.nlm.nih.gov/clinvar/variation/526246/) |

**All HGVS expressions:** `LRG_118:g.92C>T`, `LRG_119:g.11539G>A`, `LRG_119t1:c.1209G>A`, `NC_000017.10:g.76133397G>A`, `NC_000017.11:g.78137316G>A`, `NG_007879.1:g.92C>T`, `NG_007881.1:g.11539G>A`, `NM_152468.5:c.1209G>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 and, for splice-region changes, SpliceAI (below), not from a missing predictor score.
- SpliceAI predicts **donor loss** (Δ 0.24) — a splice-altering prediction the current classification does not reflect
- Conservation: phyloP 0.524, GERP -1.85, phastCons 0.052 — weakly conserved position
- CADD: **PHRED 3.865**. 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 deltas (raw): acceptor loss **0.00**, donor loss **0.24**, acceptor gain **0.00**, donor gain **0.00**. Largest is donor loss.
- SpliceAI deltas (masked): acceptor loss **0.00**, donor loss **0.24**, acceptor gain **0.00**, donor gain **0.00**.
- Population frequency (gnomAD v4.1): grpmax **1.85%** (afr) · FAF95 1.77% · FAF99 1.74% · 1,390/75,028 in the highest group · 1,648/1,614,012 alleles overall — low-frequency (popmax 1.85%, afr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| African / African-American (grpmax) | 1.85% | 54 |
| Middle Eastern | 0.297% | 337 |
| Remaining individuals (not grpmax-eligible) | 0.154% | 651 |
| Admixed American | 0.143% | 698 |
| European (non-Finnish) | 0.00483% | 20,702 |
| Ashkenazi Jewish (not grpmax-eligible) | 0.00338% | 29,608 |

*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}

**TMC8** population constraint: LOEUF 1.201, pLI 1.2654e-24, missense-Z 0.019496; ClinGen dosage — haploinsufficiency gene assoc. with recessive phenotype, triplosensitivity 0/3. *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 **403** lies in the 'tmc domain' region; a UniProt-annotated variant site (in ev2).

AlphaFold model confidence (whole protein): pLDDT 76.77, 26% of residues very-high.

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

*Describes the biological roles of TMC8 (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:** TMC8's established molecular role includes tumor necrosis factor binding. p.Lys403= falls in the tmc domain region.


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

**Molecular function:** tumor necrosis factor binding, protein sequestering activity.

**Biological process:** intracellular zinc ion homeostasis, regulation of tumor necrosis factor-mediated signaling pathway, negative regulation of protein-containing complex assembly, negative regulation of protein binding, positive regulation of apoptotic process, negative regulation of canonical NF-kappaB signal transduction.

## Clinical significance {#significance}

**Benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2026-01-27.

**Submitter consensus:** unanimous (3/3 Benign).

**Submission history:** 3 submissions (2023–2026); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Breakthrough Genomics, Breakthrough Genomics | Benign | criteria provided, single submitter | not provided |  |
| PreventionGenetics, part of Exact Sciences | Benign | no assertion criteria provided | clinical testing | 2023-12-06 |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2026-01-27 |

## Associated conditions {#conditions}

[epidermodysplasia verruciformis](https://sugi.bio/atlas/disease/epidermodysplasia-verruciformis/).

**Reported phenotype names (ClinVar):** Epidermodysplasia verruciformis, TMC8-related disorder, not provided, TMC8-related condition, none provided.

## Same-residue context {#hotspot}

Residue **403** carries **1 other pathogenic ClinVar variant** — a recurrently-mutated position: [TMC8 p.Lys403fs](/variant/tmc8-p-lys403fs). *Positional co-occurrence of independent ClinVar records, not functional proof.*

## Similar variants {#similar}

Related TMC8 variant pages (same residue, condition, or type): [TMC8 p.Lys403Asn](/variant/tmc8-p-lys403asn), [TMC8 p.Lys403fs](/variant/tmc8-p-lys403fs), [TMC8 p.Lys403Arg](/variant/tmc8-p-lys403arg), [TMC8 p.Lys403Glu](/variant/tmc8-p-lys403glu), [TMC8 c.1824-1G>C](/variant/tmc8-c-1824-minus-1g-c), [TMC8 c.449-1G>T](/variant/tmc8-c-449-minus-1g-t), [TMC8 p.Arg190Ter](/variant/tmc8-p-arg190ter), [TMC8 p.Ala188Val](/variant/tmc8-p-ala188val).

### 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 526246). 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.*