# NM_000424.4(KRT5):c.991C>T (p.Arg331Cys)

https://sugi.bio/variant/krt5-p-arg331cys

## Summary

**KRT5 p.Arg331Cys (c.991C>T)** is classified **Pathogenic/Likely pathogenic** in KRT5 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-08-19). AlphaMissense: likely pathogenic (0.9298); Very rare (popmax 0.00167%, amr); Associated with epidermolysis bullosa simplex 2A, generalized severe.

**At a glance:** Pathogenic/Likely pathogenic · review: Multiple submitters · rsID rs61297109 · 6 submitters · 3 linked conditions · AlphaMissense likely pathogenic · very rare (popmax 0.00167%, amr)

## For patients & families {#patients}

This is a change in the KRT5 gene that is considered likely disease-causing, submitted by 6 submitters, and is linked to epidermolysis bullosa simplex 2A, generalized severe.

*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:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0025580/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [KRT5](https://sugi.bio/atlas/gene/KRT5/) |
| Protein change (HGVS p.) | p.Arg331Cys |
| Coding change (HGVS c.) | c.991C>T |
| MANE Select transcript | [NM_000424](https://www.ncbi.nlm.nih.gov/nuccore/NM_000424) |
| dbSNP | [rs61297109](https://www.ncbi.nlm.nih.gov/snp/rs61297109/) |
| Variant type | single nucleotide variant |
| Location | chr12:52517691-52517691 (GRCh38) |
| ClinVar | [VCV66298](https://www.ncbi.nlm.nih.gov/clinvar/variation/66298/) |

**All HGVS expressions:** `NC_000012.11:g.52911475G>A`, `NC_000012.12:g.52517691G>A`, `NG_008297.1:g.7769C>T`, `NM_000424.4:c.991C>T`

## Computational & population evidence {#evidence}

**Concordance:** 1 independent predictor **concordant** with the ClinVar classification.

- AlphaMissense **likely pathogenic** (0.9298) — concordant with the pathogenic call
- REVEL 0.723 (pathogenic-leaning) — agrees with AlphaMissense
- SaProt LLR -14.874 (damaging) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this damaging
- Conservation: phyloP 11.893, phastCons 1 — highly conserved (agrees)
- CADD: **PHRED 34.0**. 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 0.98** across the covering region of the MANE Select transcript (52,514,945–52,517,698), spanning 2,753 bp. Chi-square p 0.69. 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 (gnomAD v4.1): grpmax **0.00167%** (amr) · FAF95 0.0005% · FAF99 0.000366% · 1/60,036 in the highest group · 13/1,614,200 alleles overall — very rare (popmax 0.00167%, amr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Admixed American (grpmax) | 0.00167% | 60,036 |
| Remaining individuals (not grpmax-eligible) | 0.0016% | 62,512 |
| European (non-Finnish) | 0.000932% | 107,275 |

*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}

**KRT5** population constraint: LOEUF 0.538, pLI 0.90196, missense-Z 1.0035. *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 **331** lies in the if rod domain; a UniProt-annotated variant site (in ddd1); the 'linker 12' region; a UniProt-annotated variant site (in ebs2c).

AlphaFold model confidence (whole protein): pLDDT 68.86, 44% of residues very-high.

**2 experimental structure(s)** (PDB): [3TNU](https://www.rcsb.org/structure/3TNU), [6JFV](https://www.rcsb.org/structure/6JFV) — incl. mutant structure 6JFV.

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

*Describes the biological roles of KRT5 (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:** KRT5's established molecular role includes scaffold protein binding. p.Arg331Cys falls in the if rod domain.


### Pathways affected {#pathways}

KRT5 participates in **7 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Developmental Lineage of Mammary Gland Luminal Epithelial Cells](https://reactome.org/content/detail/R-HSA-9927418) | curated |
| [Developmental Lineage of Mammary Gland Myoepithelial Cells](https://reactome.org/content/detail/R-HSA-9927432) | curated |
| [Developmental Lineage of Mammary Stem Cells](https://reactome.org/content/detail/R-HSA-9938206) | curated |
| [Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin](https://reactome.org/content/detail/R-HSA-9725554) | curated |
| [Formation of the cornified envelope](https://reactome.org/content/detail/R-HSA-6809371) | curated |
| [Keratinization](https://reactome.org/content/detail/R-HSA-6805567) | curated |
| [Type I hemidesmosome assembly](https://reactome.org/content/detail/R-HSA-446107) | curated |

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

**Molecular function:** scaffold protein binding.

## Clinical significance {#significance}

**Pathogenic/Likely pathogenic** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2026-08-19.

**Submitter consensus:** conflicting (3 Pathogenic, 1 likely pathogenic, 1 not provided, 1 Likely pathogenic).

**Submission history:** 6 submissions (2016–2026); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Institute of Human Genetics, University of Leipzig Medical Center | likely pathogenic | criteria provided, single submitter | clinical testing | 2026-08-19 |
| Epithelial Biology;  Institute of Medical Biology, Singapore | not provided | no classification provided | not provided |  |
| Genetic Services Laboratory, University of Chicago | Pathogenic | criteria provided, single submitter | clinical testing | 2016-04-09 |
| GeneDx | Pathogenic | criteria provided, single submitter | clinical testing | 2023-05-05 |
| Zotz-Klimas Genetics Lab, MVZ Zotz Klimas | Likely pathogenic | no assertion criteria provided | clinical testing | 2023-10-09 |
| Labcorp Genetics (formerly Invitae), Labcorp | Pathogenic | criteria provided, single submitter | clinical testing | 2024-08-31 |

## Associated conditions {#conditions}

[epidermolysis bullosa simplex 2A, generalized severe](https://sugi.bio/atlas/disease/epidermolysis-bullosa-simplex-2a-generalized-severe/), [epidermolysis bullosa simplex 1C, localized](https://sugi.bio/atlas/disease/epidermolysis-bullosa-simplex-1c-localized/), [Dowling-Degos disease 1](https://sugi.bio/atlas/disease/dowling-degos-disease-1/).

**Reported phenotype names (ClinVar):** Epidermolysis bullosa simplex 2A, generalized severe, not provided, Epidermolysis bullosa simplex 1C, localized, Dowling-Degos disease 1, Epidermolysis bullosa simplex 2, severe, Epidermolysis bullosa simplex 2, generalized severe, Epidermolysis bullosa simplex 2, Dowling-Meara type, none provided, Epidermolysis Bullosa Simplex, Weber-Cockayne Type, Weber-Cockayne Syndrome.

## Same-residue context {#hotspot}

Residue **331** carries **1 other pathogenic ClinVar variant** — a recurrently-mutated position: [KRT5 p.Arg331His](/variant/krt5-p-arg331his). *Positional co-occurrence of independent ClinVar records, not functional proof.*

## Similar variants {#similar}

Related KRT5 variant pages (same residue, condition, or type): [KRT5 p.Arg331His](/variant/krt5-p-arg331his), [KRT5 c.555+1G>A](/variant/krt5-c-555-plus-1g-a), [KRT5 p.Glu477Lys](/variant/krt5-p-glu477lys), [KRT5 p.Ile161Ser](/variant/krt5-p-ile161ser), [KRT5 p.Lys199Asn](/variant/krt5-p-lys199asn), [KRT5 p.Met327Thr](/variant/krt5-p-met327thr), [KRT5 p.Pro217Leu](/variant/krt5-p-pro217leu), [KRT5 p.Ser75Tyr](/variant/krt5-p-ser75tyr).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-14); 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 66298). 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.*