KRTAP24-1

Summary

KRTAP24-1 (keratin associated protein 24-1, HGNC:33902) is a protein-coding gene on chromosome 21q22.11, encoding Keratin-associated protein 24-1 (Q3LI83). In the hair cortex, hair keratin intermediate filaments are embedded in an interfilamentous matrix, consisting of hair keratin-associated proteins (KRTAP), which are essential for the formation of a rigid and resistant hair shaft through their extensive disulfide bond cross-link….

Predicted to enable structural molecule activity. Predicted to be located in cytosol.

Source: NCBI Gene 643803 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 38 total
• MANE Select transcript: NM_001085455

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33902
Approved symbol	KRTAP24-1
Name	keratin associated protein 24-1
Location	21q22.11
Locus type	gene with protein product
Status	Approved
Aliases	KAP24.1
Ensembl gene	ENSG00000188694
Ensembl biotype	protein_coding
OMIM	618927
Entrez	643803

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000340345

RefSeq mRNA: 1 — MANE Select: NM_001085455 NM_001085455

CCDS: CCDS42915

Canonical transcript exons

ENST00000340345 — 1 exons

Exon	Start	End
ENSE00001384913	30281309	30282950

Expression profiles

Bgee: expression breadth tissue_specific, 6 present calls, max score 37.20.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0147 / max 26.5115, expressed in 1 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
190116	0.0147	1

Top tissues by expression

132 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
sural nerve	UBERON:0015488	35.60	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
skin of abdomen	UBERON:0001416	32.52	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
zone of skin	UBERON:0000014	30.89	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
skin of leg	UBERON:0001511	29.71	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
monocyte	CL:0000576	28.86	gold quality
liver	UBERON:0002107	28.81	gold quality
leukocyte	CL:0000738	28.74	gold quality
duodenum	UBERON:0002114	28.14	gold quality
lymph node	UBERON:0000029	27.57	gold quality
tonsil	UBERON:0002372	27.05	gold quality
blood	UBERON:0000178	26.98	gold quality
urinary bladder	UBERON:0001255	26.67	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
right lung	UBERON:0002167	26.23	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
placenta	UBERON:0001987	25.81	gold quality
muscle of leg	UBERON:0001383	25.58	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.13

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

53 targeting KRTAP24-1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-196A-5P	100.00	68.16	684
HSA-MIR-196B-5P	100.00	68.16	681
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-12119	99.87	68.35	1653
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-3180-5P	99.82	69.12	2422
HSA-MIR-4677-5P	99.70	70.09	1940
HSA-MIR-379-3P	99.69	69.60	1524
HSA-MIR-411-3P	99.69	69.63	1524
HSA-MIR-466	99.67	70.85	2863
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-4649-3P	99.56	66.90	1783
HSA-MIR-7159-5P	99.53	72.12	2472
HSA-MIR-4672	99.50	71.58	2893
HSA-MIR-6740-3P	99.48	68.49	1392
HSA-MIR-1276	99.36	68.18	1642
HSA-MIR-525-5P	99.35	66.85	1615
HSA-MIR-520A-5P	99.35	66.72	1632
HSA-MIR-6128	99.33	67.83	1581
HSA-MIR-4311	99.31	70.47	3041
HSA-MIR-3191-5P	99.24	66.52	1722
HSA-MIR-7974	99.24	65.48	1137
HSA-MIR-6739-3P	99.22	68.84	1843
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-6809-5P	99.13	68.45	1223

Literature-anchored findings (GeneRIF, showing 1)

• In situ hybridization and indirect immunofluorescence microscopy studies using an antibody derived from KAP24.1 demonstrated specific expression in the middle/upper hair cuticle. (PMID:17235325)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Krtap24-1	ENSMUSG00000050239
rattus_norvegicus	Krtap24-1	ENSRNOG00000048374

Paralogs (3): KRTAP3-3 (ENSG00000212899), KRTAP3-2 (ENSG00000212900), KRTAP3-1 (ENSG00000212901)

Protein

Protein identifiers

Keratin-associated protein 24-1 — Q3LI83 (reviewed: Q3LI83)

All UniProt accessions (1): Q3LI83

UniProt curated annotations — full annotation on UniProt →

Function. In the hair cortex, hair keratin intermediate filaments are embedded in an interfilamentous matrix, consisting of hair keratin-associated proteins (KRTAP), which are essential for the formation of a rigid and resistant hair shaft through their extensive disulfide bond cross-linking with abundant cysteine residues of hair keratins. The matrix proteins include the high-sulfur and high-glycine-tyrosine keratins.

Subunit / interactions. Interacts with hair keratins.

Tissue specificity. Specific expression in the middle/upper hair cuticle.

Miscellaneous. Has a low cysteine content when compared to the majority of known KAP family members. Possesses several C-terminal tyrosine-containing tandem decameric repeat structures.

Similarity. Belongs to the PMG family.

RefSeq proteins (1): NP_001078924* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007659	Keratin_matx	Family
IPR007951	KRTAP_PMG	Family

Pfam: PF05287

UniProt features (8 total): repeat 6, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q3LI83-F1	40.46	0.00

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-6805567	Keratinization
R-HSA-1266738	Developmental Biology

MSigDB gene sets: 23 (showing top): chr21q22, GOCC_INTERMEDIATE_FILAMENT_CYTOSKELETON, GOCC_KERATIN_FILAMENT, GOMF_STRUCTURAL_MOLECULE_ACTIVITY, GOCC_SUPRAMOLECULAR_COMPLEX, GOCC_POLYMERIC_CYTOSKELETAL_FIBER, REACTOME_KERATINIZATION, GOCC_SUPRAMOLECULAR_POLYMER, MIR466, MIR7159_5P, MIR4789_3P, MIR4291, MIR589_3P, MIR518C_5P, MIR4478

GO Biological Process (0):

GO Molecular Function (1): structural molecule activity (GO:0005198)

GO Cellular Component (3): cytosol (GO:0005829), keratin filament (GO:0045095), intermediate filament (GO:0005882)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Developmental Biology	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
molecular_function	1
cytoplasm	1
cellular anatomical structure	1
intermediate filament	1
intermediate filament cytoskeleton	1
polymeric cytoskeletal fiber	1

Protein interactions and networks

STRING

202 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KRTAP24-1	KRTAP20-1	Q3LI63	871
KRTAP24-1	KRTAP13-3	Q3SY46	860
KRTAP24-1	KRTAP15-1	Q3LI76	857
KRTAP24-1	KRTAP27-1	Q3LI81	847
KRTAP24-1	KRTAP22-1	Q3MIV0	846
KRTAP24-1	KRTAP7-1	Q8IUC3	841
KRTAP24-1	KRTAP20-2	Q3LI61	830
KRTAP24-1	SCYGR1	A0A286YEY9	822
KRTAP24-1	KRTAP8-1	Q8IUC2	803
KRTAP24-1	KRTAP6-2	Q3LI66	795
KRTAP24-1	KRTAP25-1	Q3LHN0	770
KRTAP24-1	KRTAP6-3	Q3LI67	763
KRTAP24-1	KRTAP13-1	Q8IUC0	761
KRTAP24-1	KRTAP11-1	Q8IUC1	736
KRTAP24-1	KRTAP6-1	Q3LI64	723

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A1A580, A2A591, A2A5X4, A2A5X5, A8MUX0, A8MX34, B2RUR4, O13152, O93499, O93500, P02444, P02445, P02446, P02447, P02449, P02450, P02451, P04458, P07521, P08335, P0DV60, P20307, P20308, P25692, P60329, Q24JX8, Q24JX9, Q3LI81, Q3LI83, Q4KL71, Q5T749, Q5T750, Q5TA77, Q6PEX3, Q6R648, Q6S343, Q7TQM5, Q8IUC1, Q92012, Q98U05

Diamond homologs: Q3LI83, Q8IUC1, Q9D7N2, A8MUX0, Q4W7G7, Q4W7G8, Q4W7G9, Q6R648, Q9BYR6, Q9BYR7, Q6PEX3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

38 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	33
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

94 predictions. Top by Δscore:

Variant	Effect	Δscore
21:30281632:A:T	acceptor_gain	0.7700
21:30281922:T:TG	acceptor_gain	0.6800
21:30281908:CAT:C	acceptor_gain	0.6400
21:30281910:T:TC	acceptor_gain	0.5800
21:30282340:CAG:C	acceptor_gain	0.5200
21:30282706:CAG:C	donor_gain	0.4700
21:30282343:C:CC	acceptor_gain	0.4600
21:30282552:ATAC:A	donor_loss	0.4600
21:30282553:TA:T	donor_loss	0.4600
21:30281907:CCAT:C	acceptor_gain	0.4500
21:30282550:ACAT:A	donor_loss	0.4500
21:30281970:A:T	acceptor_gain	0.4300
21:30282554:AC:A	donor_gain	0.4200
21:30282555:CC:C	donor_gain	0.4200
21:30282733:TC:T	donor_gain	0.4000
21:30282554:A:AC	donor_gain	0.3900
21:30282554:ACC:A	donor_gain	0.3900
21:30282555:C:CC	donor_gain	0.3900
21:30282555:CCC:C	donor_gain	0.3900
21:30282114:A:AC	donor_gain	0.3800
21:30282555:CCCA:C	donor_gain	0.3700
21:30282342:GC:G	acceptor_loss	0.3600
21:30282344:T:TC	acceptor_loss	0.3600
21:30282345:G:C	acceptor_loss	0.3600
21:30282352:A:AC	acceptor_loss	0.3600
21:30282354:A:C	acceptor_loss	0.3600
21:30282347:TGGAA:T	acceptor_loss	0.3500
21:30282348:GGAAA:G	acceptor_loss	0.3500
21:30282555:CCCAT:C	donor_gain	0.3400
21:30282001:G:GT	acceptor_gain	0.3300

AlphaMissense

1657 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
21:30282219:A:C	F238L	0.963
21:30282219:A:T	F238L	0.963
21:30282221:A:G	F238L	0.963
21:30282767:A:G	W56R	0.960
21:30282767:A:T	W56R	0.960
21:30282765:C:A	W56C	0.948
21:30282765:C:G	W56C	0.948
21:30282786:A:C	S49R	0.898
21:30282786:A:T	S49R	0.898
21:30282788:T:G	S49R	0.898
21:30282763:A:G	L57P	0.846
21:30282766:C:G	W56S	0.845
21:30282206:A:C	Y243D	0.823
21:30282757:T:A	D59V	0.810
21:30282767:A:C	W56G	0.808
21:30282207:C:A	R242S	0.806
21:30282207:C:G	R242S	0.806
21:30282249:G:C	F228L	0.802
21:30282249:G:T	F228L	0.802
21:30282251:A:G	F228L	0.802
21:30282220:A:G	F238S	0.772
21:30282775:C:A	G53V	0.771
21:30282769:A:G	L55P	0.764
21:30282206:A:G	Y243H	0.757
21:30282208:C:A	R242M	0.756
21:30282225:A:C	S236R	0.752
21:30282225:A:T	S236R	0.752
21:30282227:T:G	S236R	0.752
21:30282202:A:G	L244S	0.751
21:30282776:C:G	G53R	0.751

dbSNP variants (sampled 300 via entrez): RS1002802655 (21:30281290 G>A), RS1002891246 (21:30283179 A>C), RS1003182482 (21:30281548 C>A,T), RS1004527050 (21:30281477 T>G), RS1006549910 (21:30280948 A>G,T), RS1008156496 (21:30281892 G>A), RS1008922308 (21:30281977 G>A), RS1009732071 (21:30280849 A>G), RS1011818190 (21:30282231 T>C), RS1012120252 (21:30284581 A>G), RS1012360641 (21:30283262 C>G), RS1012728506 (21:30281575 G>A,T), RS1012964 (21:30284372 G>A), RS1013461127 (21:30284530 A>G,T), RS1015001325 (21:30283892 T>C)

Disease associations

OMIM: gene MIM:618927 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases methylation	1
Benzo(a)pyrene	decreases methylation, affects methylation	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.