KRTAP4-2

Chr 17

keratin associated protein 4-2

Also known as: KAP4.2, KRTAP4.2

NCBI Gene: 85291UniProt: Q9BYR5

This protein is a member of the keratin-associated protein (KAP) family. The KAP proteins form a matrix of keratin intermediate filaments which contribute to the structure of hair fibers. KAP family members appear to have unique, family-specific amino- and carboxyl-terminal regions and are subdivided into three multi-gene families according to amino acid composition: the high sulfur, the ultrahigh sulfur, and the high tyrosine/glycine KAPs. This protein is a member of the ultrahigh sulfur KAP family and the gene is localized to a cluster of KAPs at 17q12-q21. [provided by RefSeq, Jul 2008]

39
ClinVar variants
7
Pathogenic / LP
0.01
pLI score
-0.3
Missense Z
1.95
LOEUF
0
Active trials
Clinical Summary— KRTAP4-2
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.01) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
7 Pathogenic / Likely Pathogenic· 29 VUS of 39 total submissions
Some data sources returned errors (1)

ensembl: Error: Ensembl fetch failed: 500 for https://rest.ensembl.org/lookup/symbol/homo_sapiens/KRTAP4-2?content-type=application/json&expand=1

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.95LOEUF
pLI 0.012
Z-score -1.18
OE 2.40 (0.55–1.95)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.27Z-score
OE missense 1.09 (0.91–1.30)
85 obs / 78.3 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.2.40 (0.55–1.95)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.09 (0.91–1.30)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.36
0≤1.21.6
LoF obs/exp: 2 / 0.8Missense obs/exp: 85 / 78.3Syn Z: -1.51

ClinVar Variant Classifications

39 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic7
VUS29
Likely Benign3
7
Pathogenic
29
VUS
3
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
7
0
7
Likely Pathogenic
0
0
0
0
0
VUS
0
28
1
0
29
Likely Benign
0
1
2
0
3
Benign
0
0
0
0
0
Total02910039

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

KRTAP4-2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype

OMIM

No OMIM entries found.

Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

Top 5 resultsSearch Europe PMC ↗
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
DUSP5 and PHLDA1 mutations in mature cystic teratomas of the ovary identified on whole-exome sequencing may explain teratoma characteristics
Wang WC et al.·Hum Genomics
2022
Disorganization of Transcriptional Regulation and Alteration of Keratin Family Gene Expression in Hairy Ear Mice.
Ahn B et al.·Genes (Basel)
2026
Identification of gene expression biomarkers to predict clinical response to methotrexate in patients with rheumatoid arthritis
Palmowski A et al.·Clin Rheumatol
2023Cohort
Human identification of single hair shaft using a mass spectrometry mRNA typing system.
Fan J et al.·Forensic Sci Int Genet
2024
Transcriptome associated with single-cell analysis reveal the role of S-palmitoylation in coronary artery disease
Xing Y et al.·Sci Rep
2025
Ancient lineages of the keratin-associated protein (KRTAP) genes and their co-option in the evolution of the hair follicle
Litman T et al.·BMC Ecol Evol
2023
A Giant Mixed Infiltrative Angiolipoma of the Back with Venous Malformation- A Case Report and Related Gene Mutation Detection
Zhao F et al.·Clin Cosmet Investig Dermatol
2023Case report
The importance of escalating molecular diagnostics in patients with low-grade pediatric brain cancer
Al Assaad M et al.·Cold Spring Harb Mol Case Stud
2023Cohort
DNA methylation variations in familial female and male breast cancer
Abeni E et al.·Oncol Lett
2021
Identification of the Key Genes Associated with Different Hair Types in the Inner Mongolia Cashmere Goat
Gong G et al.·Animals (Basel)
2022
Top 10 full-text resultsSearch PubTator3 ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients