KRTAP9-3

Summary

KRTAP9-3 (keratin associated protein 9-3, HGNC:16927) is a protein-coding gene on chromosome 17q21.2, encoding Keratin-associated protein 9-3 (Q9BYQ3). 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….

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.

Source: NCBI Gene 83900 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 47 total
• MANE Select transcript: NM_031962

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16927
Approved symbol	KRTAP9-3
Name	keratin associated protein 9-3
Location	17q21.2
Locus type	gene with protein product
Status	Approved
Aliases	KAP9.3
Ensembl gene	ENSG00000204873
Ensembl biotype	protein_coding
Entrez	83900

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000411528

RefSeq mRNA: 1 — MANE Select: NM_031962 NM_031962

CCDS: CCDS11385

Canonical transcript exons

ENST00000411528 — 1 exons

Exon	Start	End
ENSE00001474938	41232449	41233454

Expression profiles

Bgee: expression breadth broad, 24 present calls, max score 41.54.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0312 / max 32.8238, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
160818	0.0312	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
skin of abdomen	UBERON:0001416	41.54	gold quality
zone of skin	UBERON:0000014	39.48	gold quality
skin of leg	UBERON:0001511	38.15	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
sural nerve	UBERON:0015488	36.76	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
right lung	UBERON:0002167	35.49	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
stromal cell of endometrium	CL:0002255	29.87	gold quality
muscle of leg	UBERON:0001383	29.60	gold quality
gastrocnemius	UBERON:0001388	29.43	gold quality
blood	UBERON:0000178	29.38	gold quality
prefrontal cortex	UBERON:0000451	29.23	gold quality
duodenum	UBERON:0002114	28.14	gold quality
monocyte	CL:0000576	27.96	silver quality
leukocyte	CL:0000738	27.93	silver 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
placenta	UBERON:0001987	25.81	gold quality
urinary bladder	UBERON:0001255	25.72	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

37 targeting KRTAP9-3, 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-3646	100.00	73.56	5283
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-3605-5P	99.96	67.12	932
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-518A-5P	99.70	69.01	2209
HSA-MIR-527	99.70	69.01	2209
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-6832-5P	99.58	64.82	1132
HSA-MIR-4761-5P	99.51	66.69	804
HSA-MIR-186-3P	99.51	66.24	1685
HSA-MIR-3123	99.47	67.15	2693
HSA-MIR-548B-3P	99.38	67.26	1000
HSA-MIR-6882-5P	99.35	71.13	1206
HSA-MIR-892C-5P	99.16	70.56	2116
HSA-MIR-3160-3P	99.07	64.78	955
HSA-MIR-922	99.02	67.23	1838
HSA-MIR-3619-5P	99.00	68.87	2308
HSA-MIR-6770-5P	98.97	66.76	1853
HSA-MIR-3145-3P	98.85	69.07	2031
HSA-MIR-214-3P	98.71	68.12	2128
HSA-MIR-761	98.71	68.07	2051
HSA-MIR-6796-3P	98.68	65.49	689
HSA-MIR-6728-3P	98.63	67.63	1534
HSA-MIR-3928-5P	98.50	67.48	980
HSA-MIR-6806-3P	98.50	67.31	980
HSA-MIR-6873-5P	98.45	66.14	1417
HSA-MIR-302F	98.44	69.02	1776
HSA-MIR-1262	98.17	66.52	757
HSA-MIR-4701-3P	98.17	66.25	788
HSA-MIR-6736-5P	98.17	66.43	760

Cross-species orthologs

0 orthologs

Paralogs (47): KRTAP4-4 (ENSG00000171396), KRTAP9-7 (ENSG00000180386), KRTAP5-5 (ENSG00000185940), KRTAP12-1 (ENSG00000187175), KRTAP9-8 (ENSG00000187272), KRTAP10-8 (ENSG00000187766), KRTAP10-6 (ENSG00000188155), KRTAP1-1 (ENSG00000188581), KRTAP10-12 (ENSG00000189169), KRTAP4-3 (ENSG00000196156), KRTAP9-9 (ENSG00000198083), KRTAP4-6 (ENSG00000198090), KRTAP4-5 (ENSG00000198271), KRTAP4-1 (ENSG00000198443), KRTAP4-8 (ENSG00000204880), KRTAP1-4 (ENSG00000204887), KRTAP12-3 (ENSG00000205439), KRTAP10-2 (ENSG00000205445), KRTAP5-6 (ENSG00000205864), KRTAP5-2 (ENSG00000205867), KRTAP16-1 (ENSG00000212657), KRTAP9-6 (ENSG00000212659), KRTAP4-11 (ENSG00000212721), KRTAP4-9 (ENSG00000212722), KRTAP2-3 (ENSG00000212724), KRTAP2-1 (ENSG00000212725), KRTAP10-3 (ENSG00000212935), KRTAP4-12 (ENSG00000213416), KRTAP2-4 (ENSG00000213417), KRTAP2-2 (ENSG00000214518), KRTAP10-4 (ENSG00000215454), KRTAP10-1 (ENSG00000215455), KRTAP10-9 (ENSG00000221837), KRTAP1-5 (ENSG00000221852), KRTAP10-10 (ENSG00000221859), KRTAP12-2 (ENSG00000221864), KRTAP1-3 (ENSG00000221880), KRTAP9-2 (ENSG00000239886), KRTAP9-1 (ENSG00000240542), KRTAP4-7 (ENSG00000240871)

Protein

Protein identifiers

Keratin-associated protein 9-3 — Q9BYQ3 (reviewed: Q9BYQ3)

Alternative names: Keratin-associated protein 9.3, Ultrahigh sulfur keratin-associated protein 9.3

All UniProt accessions (1): Q9BYQ3

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 KRTAP type 9 family.

RefSeq proteins (1): NP_114168* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002494	KAP	Family

Pfam: PF13885

UniProt features (18 total): repeat 16, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BYQ3-F1	36.86	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: 20 (showing top): GOCC_INTERMEDIATE_FILAMENT_CYTOSKELETON, GOCC_KERATIN_FILAMENT, GOCC_SUPRAMOLECULAR_COMPLEX, GOCC_POLYMERIC_CYTOSKELETAL_FIBER, REACTOME_KERATINIZATION, GOCC_SUPRAMOLECULAR_POLYMER, MIR3662, MIR494_3P, MIR892C_5P, MIR518A_5P_MIR527, MIR6770_5P, MIR6806_3P, MIR3928_5P, MIR3605_5P, MIR127_5P

GO Biological Process (0):

GO Molecular Function (2): identical protein binding (GO:0042802), protein binding (GO:0005515)

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
protein binding	1
binding	1
cytoplasm	1
cellular anatomical structure	1
intermediate filament	1
intermediate filament cytoskeleton	1
polymeric cytoskeletal fiber	1

Protein interactions and networks

STRING

248 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KRTAP9-3	KRTAP3-1	Q9BYR8	587
KRTAP9-3	KRTAP13-3	Q3SY46	544
KRTAP9-3	KRTAP17-1	Q9BYP8	507
KRTAP9-3	KRTAP3-3	Q9BYR6	467
KRTAP9-3	KRT33B	Q14525	431
KRTAP9-3	KRT83	P78385	378
KRTAP9-3	KRT27	Q7Z3Y8	369
KRTAP9-3	KRT86	P78387	369
KRTAP9-3	KRT34	O76011	359
KRTAP9-3	KRT71	Q3SY84	353
KRTAP9-3	KRT31	Q15323	324
KRTAP9-3	HID1	Q8IV36	300
KRTAP9-3	FAM234B	A2RU67	250
KRTAP9-3	SRARP	Q8NEQ6	246
KRTAP9-3	ATOSA	Q32MH5	223

IntAct

431 interactions, top by confidence:

A	B	Type	Score
CDK12	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.000
CDC20	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.000
NR1D2	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.000
ZNF414	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.000
KRTAP9-3	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.000
LCE2A	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.000
NTM	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.000
VASN	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.000
LCE3C	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.000
CHRNG	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.000
WNT11	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.000
KRTAP9-3	KRTAP5-9	psi-mi:“MI:0915”(physical association)	0.000
KRTAP9-3	GLRX3	psi-mi:“MI:0915”(physical association)	0.000
KRTAP9-3	ATN1	psi-mi:“MI:0915”(physical association)	0.000
KRTAP9-3	KRTAP2-4	psi-mi:“MI:0915”(physical association)	0.000
KRTAP9-3	ADAMTSL4	psi-mi:“MI:0915”(physical association)	0.000
FBXW5	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.000
KRTAP5-3	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.000
ZNF497	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.000
SLC25A18	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.000
CCER1	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.000
MAPKBP1	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.000
KRTAP9-3	KRTAP10-5	psi-mi:“MI:0915”(physical association)	0.000
DOCK2	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.000
PRKAB2	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.000
CRCT1	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.000
KRTAP10-10	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.000
LCE1A	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.000
KRTAP9-3	NOTCH2NLC	psi-mi:“MI:0915”(physical association)	0.000
KRTAP9-3	RGS20	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (140): KRTAP9-3 (Affinity Capture-MS), KRTAP9-3 (Affinity Capture-MS), KRTAP9-3 (Two-hybrid), KRTAP9-3 (Two-hybrid), KRTAP9-3 (Two-hybrid), KRTAP9-3 (Two-hybrid), KRTAP9-3 (Two-hybrid), KRTAP9-3 (Two-hybrid), KRTAP9-3 (Two-hybrid), KRTAP9-3 (Two-hybrid), KRTAP9-3 (Two-hybrid), KRTAP9-3 (Two-hybrid), KRTAP9-3 (Two-hybrid), KRTAP9-3 (Two-hybrid), KRTAP9-3 (Two-hybrid)

ESM2 similar proteins: A5A6P5, A6QP35, A8MTY7, A8MVA2, A8MXZ3, O75690, P02438, P02441, P02442, P02443, P08131, P0C7H8, P26371, P59990, P59991, P60014, P60331, P60368, P60369, P60370, P60371, P60372, P60409, P60410, P60411, P60412, P60413, Q05B44, Q07627, Q3V2C1, Q6L8G4, Q6L8G8, Q6L8G9, Q6L8H2, Q701N4, Q8IUG1, Q9BQ66, Q9BYP9, Q9BYQ0, Q9BYQ2

Diamond homologs: A5A6P5, Q9BYP9, Q9BYQ0, Q9BYQ2, Q9BYQ3, Q9BYQ4, A8MTY7, A8MVA2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 120 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Keratinization	44	28.2×	1e-52
Formation of the cornified envelope	18	18.2×	2e-16

GO biological processes:

GO term	Partners	Fold	FDR
keratinization	17	43.7×	3e-21

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	39
Likely benign	8
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

295 predictions. Top by Δscore:

Variant	Effect	Δscore
17:41233277:G:GT	donor_gain	0.7900
17:41233181:C:G	acceptor_gain	0.7500
17:41233112:T:G	acceptor_gain	0.7400
17:41233180:A:AG	acceptor_gain	0.7300
17:41233186:T:TA	acceptor_gain	0.7200
17:41233187:G:A	acceptor_gain	0.6700
17:41232729:T:TA	donor_gain	0.6500
17:41232730:A:AA	donor_gain	0.6500
17:41233373:AC:A	acceptor_gain	0.6500
17:41233180:ACCTT:A	acceptor_gain	0.6400
17:41232775:C:A	donor_gain	0.6300
17:41232947:G:GG	donor_gain	0.6300
17:41232924:G:GT	donor_gain	0.6200
17:41232843:T:TA	acceptor_gain	0.6100
17:41233201:C:G	donor_gain	0.6100
17:41233141:G:T	donor_gain	0.6000
17:41233272:C:G	donor_gain	0.6000
17:41233278:A:T	donor_gain	0.6000
17:41233373:A:AG	acceptor_gain	0.5900
17:41233374:C:G	acceptor_gain	0.5900
17:41233236:C:G	donor_gain	0.5800
17:41233374:C:CA	acceptor_gain	0.5800
17:41232668:GCT:G	donor_gain	0.5600
17:41232670:T:G	donor_gain	0.5600
17:41232774:TCA:T	donor_gain	0.5600
17:41232601:C:A	donor_gain	0.5500
17:41233140:G:GT	donor_gain	0.5500
17:41232671:G:GG	donor_gain	0.5400
17:41232909:G:GT	donor_gain	0.5400
17:41233220:G:GT	donor_gain	0.5400

AlphaMissense

1053 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:41232810:A:C	R103S	0.658
17:41232810:A:T	R103S	0.658
17:41232804:C:G	C101W	0.622
17:41232934:T:C	F145L	0.616
17:41232936:C:A	F145L	0.616
17:41232936:C:G	F145L	0.616
17:41232814:T:C	C105R	0.612
17:41232847:T:C	C116R	0.579

dbSNP variants (sampled 300 via entrez): RS1001064896 (17:41232354 G>A,T), RS1002502036 (17:41231328 A>G), RS1004157836 (17:41231309 T>C), RS1004210358 (17:41231103 G>A), RS1004491104 (17:41232549 C>A,G), RS1005480270 (17:41231596 ACTT>A,ACTTCTT), RS1006161654 (17:41233456 A>G), RS1006215762 (17:41233193 T>C), RS1007808396 (17:41233716 C>A,G), RS1008285857 (17:41230477 T>C), RS1008401683 (17:41230716 T>A), RS1008619462 (17:41231635 C>T), RS1010469165 (17:41230668 A>G), RS1010797738 (17:41231868 A>G,T), RS1012400222 (17:41232742 T>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

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
hydroxyhydroquinone	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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