KRTAP9-2

Summary

KRTAP9-2 (keratin associated protein 9-2, HGNC:16926) is a protein-coding gene on chromosome 17q21.2, encoding Keratin-associated protein 9-2 (Q9BYQ4). 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 83899 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 43 total
• MANE Select transcript: NM_031961

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16926
Approved symbol	KRTAP9-2
Name	keratin associated protein 9-2
Location	17q21.2
Locus type	gene with protein product
Status	Approved
Aliases	KAP9.2
Ensembl gene	ENSG00000239886
Ensembl biotype	protein_coding
Entrez	83899

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000377721

RefSeq mRNA: 1 — MANE Select: NM_031961 NM_031961

CCDS: CCDS32651

Canonical transcript exons

ENST00000377721 — 1 exons

Exon	Start	End
ENSE00001474940	41226648	41227652

Expression profiles

Bgee: expression breadth broad, 21 present calls, max score 39.14.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
skin of abdomen	UBERON:0001416	39.14	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
zone of skin	UBERON:0000014	36.95	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
skin of leg	UBERON:0001511	35.69	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
right lung	UBERON:0002167	33.62	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
liver	UBERON:0002107	30.57	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
right lobe of liver	UBERON:0001114	28.89	gold quality
duodenum	UBERON:0002114	28.14	gold quality
muscle of leg	UBERON:0001383	28.10	gold quality
urinary bladder	UBERON:0001255	27.95	silver quality
gastrocnemius	UBERON:0001388	27.60	gold quality
lymph node	UBERON:0000029	27.57	gold quality
primary visual cortex	UBERON:0002436	27.28	gold quality
tonsil	UBERON:0002372	27.05	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
leukocyte	CL:0000738	26.43	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
monocyte	CL:0000576	26.32	gold quality
gall bladder	UBERON:0002110	25.98	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.06

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

46 targeting KRTAP9-2, 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-3613-3P	100.00	76.36	7965
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3605-5P	99.96	67.12	932
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-518A-5P	99.70	69.01	2209
HSA-MIR-527	99.70	69.01	2209
HSA-MIR-7154-5P	99.69	70.52	1900
HSA-MIR-580-3P	99.67	69.23	1841
HSA-MIR-6832-5P	99.58	64.82	1132
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-4761-5P	99.51	66.69	804
HSA-MIR-3123	99.47	67.15	2693
HSA-MIR-2392	99.43	67.50	708
HSA-MIR-4311	99.31	70.47	3041
HSA-MIR-892C-5P	99.16	70.56	2116
HSA-MIR-6510-5P	99.14	66.59	1081
HSA-MIR-922	99.02	67.23	1838
HSA-MIR-3619-5P	99.00	68.87	2308
HSA-MIR-876-3P	98.76	68.23	945
HSA-MIR-214-3P	98.71	68.12	2128
HSA-MIR-761	98.71	68.07	2051
HSA-MIR-6894-5P	98.70	63.78	809
HSA-MIR-3928-5P	98.50	67.48	980
HSA-MIR-6806-3P	98.50	67.31	980
HSA-MIR-541-5P	98.24	67.77	1181

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), KRTAP9-3 (ENSG00000204873), 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), KRTAP9-1 (ENSG00000240542), KRTAP4-7 (ENSG00000240871)

Protein

Protein identifiers

Keratin-associated protein 9-2 — Q9BYQ4 (reviewed: Q9BYQ4)

Alternative names: Keratin-associated protein 9.2, Ultrahigh sulfur keratin-associated protein 9.2

All UniProt accessions (1): Q9BYQ4

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_114167* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002494	KAP	Family

Pfam: PF13885

UniProt features (21 total): repeat 17, sequence variant 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BYQ4-F1	37.55	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: 25 (showing top): TATA_C, GOCC_INTERMEDIATE_FILAMENT_CYTOSKELETON, GOCC_KERATIN_FILAMENT, TCANNTGAY_SREBP1_01, PEDRIOLI_MIR31_TARGETS_UP, GOCC_SUPRAMOLECULAR_COMPLEX, GOCC_POLYMERIC_CYTOSKELETAL_FIBER, REACTOME_KERATINIZATION, GOCC_SUPRAMOLECULAR_POLYMER, MIR570_3P, MIR494_3P, MIR892C_5P, MIR3123, TATA_01, MIR597_3P

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

402 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KRTAP9-2	KRTAP13-1	Q8IUC0	587
KRTAP9-2	KRTAP6-1	Q3LI64	528
KRTAP9-2	SCYGR1	A0A286YEY9	527
KRTAP9-2	KRT27	Q7Z3Y8	526
KRTAP9-2	KRTAP13-2	Q52LG2	524
KRTAP9-2	KRTAP20-1	Q3LI63	507
KRTAP9-2	KRTAP19-3	Q7Z4W3	503
KRTAP9-2	A8MUN0	A8MUN0	502
KRTAP9-2	KRTAP1-4	P0C5Y4	480
KRTAP9-2	KRT39	Q6A163	479
KRTAP9-2	KRTAP19-2	Q3LHN2	476
KRTAP9-2	KRTAP13-3	Q3SY46	468
KRTAP9-2	KRTAP3-1	Q9BYR8	447
KRTAP9-2	ZNF468	Q5VIY5	444
KRTAP9-2	KRTAP6-3	Q3LI67	414

IntAct

656 interactions, top by confidence:

A	B	Type	Score
LCE1B	KRTAP9-2	psi-mi:“MI:0915”(physical association)	0.790
KRTAP9-2	LCE1B	psi-mi:“MI:0915”(physical association)	0.790
KRTAP10-9	KRTAP9-2	psi-mi:“MI:0915”(physical association)	0.740
LCE4A	KRTAP9-2	psi-mi:“MI:0915”(physical association)	0.740
KRTAP9-2	KRTAP10-9	psi-mi:“MI:0915”(physical association)	0.740
KRTAP9-2	LCE4A	psi-mi:“MI:0915”(physical association)	0.740
KRTAP9-2	PRKAB2	psi-mi:“MI:0915”(physical association)	0.720
KRTAP9-2	HOXA1	psi-mi:“MI:0915”(physical association)	0.720
KRTAP9-2	KRTAP10-11	psi-mi:“MI:0915”(physical association)	0.720
CREB5	KRTAP9-2	psi-mi:“MI:0915”(physical association)	0.720
JOSD1	KRTAP9-2	psi-mi:“MI:0915”(physical association)	0.720
LCE3E	KRTAP9-2	psi-mi:“MI:0915”(physical association)	0.720
LCE2A	KRTAP9-2	psi-mi:“MI:0915”(physical association)	0.720
KRTAP5-6	KRTAP9-2	psi-mi:“MI:0915”(physical association)	0.720
KRTAP9-2	CATSPER1	psi-mi:“MI:0915”(physical association)	0.720
KRTAP9-2	PTPMT1	psi-mi:“MI:0915”(physical association)	0.720
NTAQ1	KRTAP9-2	psi-mi:“MI:0915”(physical association)	0.720
NUFIP2	KRTAP9-2	psi-mi:“MI:0915”(physical association)	0.720
KRTAP9-2	GLRX3	psi-mi:“MI:0915”(physical association)	0.720
KRTAP5-9	KRTAP9-2	psi-mi:“MI:0915”(physical association)	0.720
OTX1	KRTAP9-2	psi-mi:“MI:0915”(physical association)	0.720
SMCP	KRTAP9-2	psi-mi:“MI:0915”(physical association)	0.720

BioGRID (183): KRTAP9-2 (Two-hybrid), KRTAP9-2 (Two-hybrid), KRTAP9-2 (Two-hybrid), KRTAP9-2 (Two-hybrid), KRTAP9-2 (Two-hybrid), KRTAP9-2 (Two-hybrid), KRTAP9-2 (Two-hybrid), KRTAP9-2 (Two-hybrid), KRTAP9-2 (Two-hybrid), KRTAP9-2 (Two-hybrid), KRTAP9-2 (Two-hybrid), KRTAP9-2 (Two-hybrid), KRTAP9-2 (Two-hybrid), KRTAP9-2 (Two-hybrid), KRTAP9-2 (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, A8MVA2, A8MTY7

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 64 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	20	24.8×	2e-21
Formation of the cornified envelope	8	15.6×	2e-06

GO biological processes:

GO term	Partners	Fold	FDR
keratinization	7	32.8×	6e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	43
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

239 predictions. Top by Δscore:

Variant	Effect	Δscore
17:41227378:A:AG	acceptor_gain	0.8300
17:41227384:T:TA	acceptor_gain	0.8300
17:41227379:C:G	acceptor_gain	0.8000
17:41227310:T:G	acceptor_gain	0.7900
17:41227376:A:AG	acceptor_gain	0.7800
17:41227475:G:GT	donor_gain	0.7600
17:41227385:G:A	acceptor_gain	0.7300
17:41227378:ACCTT:A	acceptor_gain	0.7200
17:41227339:G:T	donor_gain	0.6800
17:41226726:G:GT	donor_gain	0.6600
17:41227377:C:G	acceptor_gain	0.6400
17:41227448:TC:T	donor_gain	0.6300
17:41227338:G:GT	donor_gain	0.6100
17:41227466:GCTTC:G	donor_gain	0.6100
17:41227415:GTT:G	donor_gain	0.6000
17:41227416:TTT:T	donor_gain	0.6000
17:41227529:A:AG	acceptor_gain	0.6000
17:41227382:T:A	acceptor_gain	0.5900
17:41227408:TTCTC:T	donor_gain	0.5900
17:41227470:C:G	donor_gain	0.5900
17:41227479:T:TG	donor_gain	0.5900
17:41226836:GCT:G	donor_gain	0.5600
17:41227479:T:G	donor_gain	0.5500
17:41227107:G:GT	donor_gain	0.5400
17:41227572:T:G	acceptor_gain	0.5400
17:41226926:G:GG	donor_gain	0.5300
17:41227122:G:GT	donor_gain	0.5300
17:41227470:C:CG	donor_gain	0.5300
17:41227487:C:G	donor_gain	0.5300
17:41227571:AT:A	acceptor_gain	0.5300

AlphaMissense

1147 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:41227012:T:C	C120R	0.754
17:41227008:A:C	R118S	0.743
17:41227008:A:T	R118S	0.743
17:41227014:C:G	C120W	0.700
17:41227015:T:G	Y121D	0.699
17:41227002:C:G	C116W	0.675
17:41226874:A:C	S74R	0.652
17:41226876:C:A	S74R	0.652
17:41226876:C:G	S74R	0.652
17:41227000:T:C	C116R	0.627
17:41226790:A:C	S46R	0.621
17:41226792:C:A	S46R	0.621
17:41226792:C:G	S46R	0.621
17:41227132:T:C	F160L	0.621
17:41227134:C:A	F160L	0.621
17:41227134:C:G	F160L	0.621
17:41227045:T:C	C131R	0.611
17:41227012:T:A	C120S	0.598
17:41227013:G:C	C120S	0.598
17:41227013:G:A	C120Y	0.589
17:41227015:T:C	Y121H	0.577
17:41227047:C:G	C131W	0.577
17:41227176:C:G	C174W	0.575
17:41227022:C:A	P123H	0.568

dbSNP variants (sampled 300 via entrez): RS1000295991 (17:41238395 G>A), RS1000453506 (17:41224716 T>C), RS1000588471 (17:41224956 C>G), RS1000856489 (17:41225567 T>G), RS1001119976 (17:41238249 C>G,T), RS1001857195 (17:41226893 G>A), RS1002262875 (17:41226126 T>C), RS1002636836 (17:41237687 G>A,C), RS1003098964 (17:41237467 A>G), RS1003748641 (17:41237370 G>A), RS1004344091 (17:41226093 T>G), RS1004822199 (17:41225772 G>A), RS1005086492 (17:41226981 C>T), RS1006037565 (17:41237901 G>A,T), RS1006294509 (17:41228055 G>A)

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

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Aflatoxin B1	decreases methylation	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

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