KRTAP25-1

Summary

KRTAP25-1 (keratin associated protein 25-1, HGNC:34003) is a protein-coding gene on chromosome 21q22.11, encoding Keratin-associated protein 25-1 (Q3LHN0). 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 100131902 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 16 total
• MANE Select transcript: NM_001128598

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34003
Approved symbol	KRTAP25-1
Name	keratin associated protein 25-1
Location	21q22.11
Locus type	gene with protein product
Status	Approved
Aliases	KAP25.1
Ensembl gene	ENSG00000232263
Ensembl biotype	protein_coding
Entrez	100131902

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000416044

RefSeq mRNA: 1 — MANE Select: NM_001128598 NM_001128598

CCDS: CCDS46640

Canonical transcript exons

ENST00000416044 — 1 exons

Exon	Start	End
ENSE00001729371	30289145	30289514

Expression profiles

Bgee: expression breadth tissue_specific, 4 present calls, max score 45.85.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	45.85	silver 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
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	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
sural nerve	UBERON:0015488	30.93	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
leukocyte	CL:0000738	29.22	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
monocyte	CL:0000576	28.42	gold quality
duodenum	UBERON:0002114	28.14	gold quality
liver	UBERON:0002107	28.04	gold quality
lymph node	UBERON:0000029	27.57	gold quality
tonsil	UBERON:0002372	27.05	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
blood	UBERON:0000178	25.84	silver quality
placenta	UBERON:0001987	25.81	gold quality
urinary bladder	UBERON:0001255	25.72	gold quality
muscle of leg	UBERON:0001383	24.74	gold quality
primary visual cortex	UBERON:0002436	24.61	gold quality
superior frontal gyrus	UBERON:0002661	24.08	gold quality
pancreas	UBERON:0001264	23.89	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.99

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Paralogs (8): KRTAP11-1 (ENSG00000182591), KRTAP13-2 (ENSG00000182816), KRTAP15-1 (ENSG00000186970), KRTAP13-4 (ENSG00000186971), KRTAP26-1 (ENSG00000197683), KRTAP13-1 (ENSG00000198390), KRTAP27-1 (ENSG00000206107), KRTAP13-3 (ENSG00000240432)

Protein

Protein identifiers

Keratin-associated protein 25-1 — Q3LHN0 (reviewed: Q3LHN0)

All UniProt accessions (1): Q3LHN0

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.

Similarity. Belongs to the PMG family.

RefSeq proteins (1): NP_001122070* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007659	Keratin_matx	Family
IPR007951	KRTAP_PMG	Family

Pfam: PF05287

UniProt features (2 total): chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q3LHN0-F1	34.60	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: 8 (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

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

270 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KRTAP25-1	SCYGR1	A0A286YEY9	791
KRTAP25-1	KRTAP27-1	Q3LI81	772
KRTAP25-1	KRTAP24-1	Q3LI83	770
KRTAP25-1	KRTAP26-1	Q6PEX3	769
KRTAP25-1	KRTAP22-1	Q3MIV0	582
KRTAP25-1	KRTAP20-1	Q3LI63	582
KRTAP25-1	KRTAP6-3	Q3LI67	571
KRTAP25-1	KRTAP6-2	Q3LI66	570
KRTAP25-1	KRTAP20-2	Q3LI61	556
KRTAP25-1	KRTAP13-3	Q3SY46	540
KRTAP25-1	KRTAP6-1	Q3LI64	507
KRTAP25-1	KRTAP15-1	Q3LI76	507
KRTAP25-1	KRTAP21-2	Q3LI59	479
KRTAP25-1	A8MUN0	A8MUN0	476
KRTAP25-1	KRTAP5-6	Q6L8G9	431

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A172M4N0, A0A1B0GTH6, A0A1B0GUW6, A1A580, A1YFC1, A1YGK6, A2A5X4, A2T7F2, A4ZUB2, A6NJ88, B2RUR4, C4P6S0, G3X9U1, O48582, P02444, P02445, P02446, P02447, P02449, P02450, P07521, P08335, P20307, P20308, P79958, Q24JX8, Q3LHN0, Q3LI81, Q3LI83, Q3URU2, Q3V0C1, Q3V3Q4, Q5T749, Q5UP52, Q68FV4, Q6AYN3, Q6PEX3, Q6S343, Q7TQM5, Q80Y39

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	14
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

167 predictions. Top by Δscore:

Variant	Effect	Δscore
21:30289458:A:AC	donor_gain	0.8400
21:30289459:C:CC	donor_gain	0.8400
21:30289456:C:CT	donor_gain	0.8100
21:30289457:T:TT	donor_gain	0.8100
21:30289479:T:C	donor_gain	0.7900
21:30289470:G:GA	donor_gain	0.7700
21:30289167:CA:C	acceptor_gain	0.7500
21:30289169:C:CC	acceptor_gain	0.7500
21:30289455:A:C	donor_gain	0.7400
21:30289460:T:C	donor_gain	0.7400
21:30289469:AG:A	donor_gain	0.7300
21:30289165:GACA:G	acceptor_gain	0.7000
21:30289485:ATG:A	donor_gain	0.6900
21:30289331:GATTA:G	donor_loss	0.6700
21:30289332:ATTAC:A	donor_loss	0.6700
21:30289333:TTAC:T	donor_loss	0.6700
21:30289334:TA:T	donor_loss	0.6700
21:30289335:A:G	donor_loss	0.6700
21:30289336:C:CT	donor_loss	0.6700
21:30289467:AAAG:A	donor_gain	0.6600
21:30289468:AAG:A	donor_gain	0.6600
21:30289337:C:T	donor_loss	0.6500
21:30289350:G:C	donor_gain	0.6500
21:30289466:AAAAG:A	donor_gain	0.6200
21:30289164:AGACA:A	acceptor_gain	0.6000
21:30289166:ACAC:A	acceptor_gain	0.6000
21:30289487:G:A	donor_gain	0.6000
21:30289506:A:C	donor_gain	0.6000
21:30289335:A:AC	donor_gain	0.5900
21:30289336:C:CC	donor_gain	0.5900

AlphaMissense

690 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
21:30289242:G:C	F83L	0.772
21:30289242:G:T	F83L	0.772
21:30289244:A:G	F83L	0.772
21:30289302:G:C	F63L	0.717
21:30289302:G:T	F63L	0.717
21:30289304:A:G	F63L	0.717
21:30289272:G:C	F73L	0.672
21:30289272:G:T	F73L	0.672
21:30289274:A:G	F73L	0.672
21:30289401:A:C	F30L	0.624
21:30289401:A:T	F30L	0.624
21:30289403:A:G	F30L	0.624
21:30289407:A:C	F28L	0.621
21:30289407:A:T	F28L	0.621
21:30289409:A:G	F28L	0.621
21:30289377:A:C	F38L	0.616
21:30289377:A:T	F38L	0.616
21:30289379:A:G	F38L	0.616
21:30289221:A:C	F90L	0.598
21:30289221:A:T	F90L	0.598
21:30289223:A:G	F90L	0.598
21:30289200:A:C	F97L	0.571
21:30289200:A:T	F97L	0.571
21:30289202:A:G	F97L	0.571

dbSNP variants (sampled 300 via entrez): RS1000267576 (21:30290935 T>G), RS1002442366 (21:30290494 A>G), RS1002652327 (21:30290789 G>A), RS1003523764 (21:30288905 T>C), RS1005407482 (21:30289811 G>A,T), RS1006278077 (21:30289932 C>G,T), RS1007327994 (21:30291213 G>A), RS1007702986 (21:30291488 G>A), RS1009843266 (21:30290841 C>T), RS1010340261 (21:30291187 C>T), RS1012624269 (21:30288982 G>C), RS1013574411 (21:30290225 C>T), RS1013626682 (21:30290455 C>T), RS1014004782 (21:30288968 A>G), RS1014229514 (21:30290420 C>G)

Disease associations

OMIM: gene `` | 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

1 total (human), top 1 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases methylation, increases methylation	1

Clinical trials (associated diseases)

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