KRTAP3-2

Summary

KRTAP3-2 (keratin associated protein 3-2, HGNC:16779) is a protein-coding gene on chromosome 17q21.2, encoding Keratin-associated protein 3-2 (Q9BYR7). 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 high sulfur KAP family and the gene is localized to a cluster of KAPs at 17q12-q21.

Source: NCBI Gene 83897 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 18 total
• MANE Select transcript: NM_031959

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16779
Approved symbol	KRTAP3-2
Name	keratin associated protein 3-2
Location	17q21.2
Locus type	gene with protein product
Status	Approved
Aliases	KAP3.2
Ensembl gene	ENSG00000212900
Ensembl biotype	protein_coding
Entrez	83897

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000391587

RefSeq mRNA: 1 — MANE Select: NM_031959 NM_031959

CCDS: CCDS32644

Canonical transcript exons

ENST00000391587 — 1 exons

Exon	Start	End
ENSE00001509366	40999193	40999906

Expression profiles

Bgee: expression breadth broad, 70 present calls, max score 77.98.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1487 / max 54.2817, expressed in 27 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
165862	0.1487	27

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	77.98	silver quality
lower esophagus mucosa	UBERON:0035834	74.21	gold quality
skin of abdomen	UBERON:0001416	57.88	gold quality
esophagus mucosa	UBERON:0002469	55.93	gold quality
zone of skin	UBERON:0000014	55.09	gold quality
skin of leg	UBERON:0001511	53.50	gold quality
right lung	UBERON:0002167	43.31	gold quality
esophagus	UBERON:0001043	42.08	gold quality
colonic epithelium	UBERON:0000397	42.02	gold quality
minor salivary gland	UBERON:0001830	38.22	gold quality
mucosa of transverse colon	UBERON:0004991	37.74	silver quality
saliva-secreting gland	UBERON:0001044	37.42	gold quality
gall bladder	UBERON:0002110	37.05	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	35.93	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
duodenum	UBERON:0002114	34.01	gold quality
vagina	UBERON:0000996	33.61	gold quality
right testis	UBERON:0004534	33.51	silver quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
islet of Langerhans	UBERON:0000006	32.61	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	31.64	silver quality
muscle tissue	UBERON:0002385	31.06	gold quality
gastrocnemius	UBERON:0001388	31.01	gold quality
muscle of leg	UBERON:0001383	30.97	gold quality
small intestine	UBERON:0002108	30.92	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.27

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

21 targeting KRTAP3-2, 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-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-3679-3P	99.64	69.88	1599
HSA-MIR-4649-3P	99.56	66.90	1783
HSA-MIR-3128	99.50	67.85	1258
HSA-MIR-1912-3P	99.32	67.40	936
HSA-MIR-6828-5P	99.31	69.21	1433
HSA-MIR-548AS-3P	99.12	69.12	2294
HSA-MIR-1295B-5P	99.03	67.50	810
HSA-MIR-3130-5P	98.14	66.00	711
HSA-MIR-22-5P	97.67	68.92	1355
HSA-MIR-4482-5P	97.53	65.68	598
HSA-MIR-6839-5P	96.74	68.29	1088
HSA-MIR-378J	96.44	66.20	1020
HSA-MIR-3914	94.91	65.77	643

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Krtap3-2	ENSMUSG00000069721
mus_musculus	Krtap3-3	ENSMUSG00000069722
rattus_norvegicus	Krtap3-2	ENSRNOG00000083895
rattus_norvegicus	Krtap3-3	ENSRNOG00000084880

Paralogs (3): KRTAP24-1 (ENSG00000188694), KRTAP3-3 (ENSG00000212899), KRTAP3-1 (ENSG00000212901)

Protein

Protein identifiers

Keratin-associated protein 3-2 — Q9BYR7 (reviewed: Q9BYR7)

Alternative names: High sulfur keratin-associated protein 3.2, Keratin-associated protein 3.2

All UniProt accessions (1): Q9BYR7

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 3 family.

RefSeq proteins (1): NP_114165* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007659	Keratin_matx	Family

Pfam: PF04579

UniProt features (8 total): repeat 3, sequence variant 3, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BYR7-F1	45.30	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): GOZGIT_ESR1_TARGETS_DN, GOCC_INTERMEDIATE_FILAMENT_CYTOSKELETON, GOCC_KERATIN_FILAMENT, GOMF_STRUCTURAL_MOLECULE_ACTIVITY, GOCC_SUPRAMOLECULAR_COMPLEX, GOCC_POLYMERIC_CYTOSKELETAL_FIBER, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, REACTOME_KERATINIZATION, GOCC_SUPRAMOLECULAR_POLYMER, MIR4659A_3P_MIR4659B_3P, MIR548AA_MIR548AP_3P_MIR548T_3P, MIR539_5P, MIR3679_3P, MIR7162_3P, MIR4649_3P

GO Biological Process (0):

GO Molecular Function (2): structural molecule activity (GO:0005198), 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
molecular_function	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

324 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KRTAP3-2	KRTAP1-4	P0C5Y4	630
KRTAP3-2	KRTAP2-3	P0C7H8	571
KRTAP3-2	KRTAP1-1	Q07627	557
KRTAP3-2	KRT27	Q7Z3Y8	543
KRTAP3-2	KRTAP4-3	Q9BYR4	541
KRTAP3-2	KRTAP1-5	Q9BYS1	538
KRTAP3-2	KRTAP6-2	Q3LI66	522
KRTAP3-2	KRTAP1-3	Q8IUG1	507
KRTAP3-2	KRTAP4-1	Q9BYQ7	507
KRTAP3-2	KRT31	Q15323	498
KRTAP3-2	KRTAP24-1	Q3LI83	490
KRTAP3-2	KRTAP13-3	Q3SY46	490
KRTAP3-2	KRTAP16-1	A8MUX0	480
KRTAP3-2	KRTAP2-1	Q9BYU5	480
KRTAP3-2	KRTAP6-3	Q3LI67	479

IntAct

279 interactions, top by confidence:

A	B	Type	Score
KRTAP3-2	LCE1B	psi-mi:“MI:0915”(physical association)	0.830
LCE1B	KRTAP3-2	psi-mi:“MI:0915”(physical association)	0.830
OTX1	KRTAP3-2	psi-mi:“MI:0915”(physical association)	0.780
KRTAP3-2	YIPF3	psi-mi:“MI:0915”(physical association)	0.780
KRTAP3-2	OTX1	psi-mi:“MI:0915”(physical association)	0.780
YIPF3	KRTAP3-2	psi-mi:“MI:0915”(physical association)	0.780
NUFIP2	KRTAP3-2	psi-mi:“MI:0915”(physical association)	0.720
KRTAP10-5	KRTAP3-2	psi-mi:“MI:0915”(physical association)	0.720
CREB5	KRTAP3-2	psi-mi:“MI:0915”(physical association)	0.720
LCE3C	KRTAP3-2	psi-mi:“MI:0915”(physical association)	0.720
KRTAP3-2	LCE4A	psi-mi:“MI:0915”(physical association)	0.720
KRTAP3-2	CREB5	psi-mi:“MI:0915”(physical association)	0.720
KRTAP3-2	NUFIP2	psi-mi:“MI:0915”(physical association)	0.720
KRTAP3-2	KRTAP10-5	psi-mi:“MI:0915”(physical association)	0.720

BioGRID (92): KRTAP3-2 (Two-hybrid), KRTAP3-2 (Two-hybrid), KRTAP3-2 (Two-hybrid), KRTAP3-2 (Two-hybrid), KRTAP3-2 (Two-hybrid), KRTAP3-2 (Two-hybrid), KRTAP3-2 (Two-hybrid), KRTAP3-2 (Two-hybrid), KRTAP3-2 (Two-hybrid), KRTAP3-2 (Two-hybrid), KRTAP3-2 (Two-hybrid), KRTAP3-2 (Two-hybrid), KRTAP3-2 (Two-hybrid), KRTAP9-2 (Two-hybrid), DHRS1 (Two-hybrid)

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: A2A591, P02444, P02445, P02446, P02447, Q24JX8, Q24JX9, Q6S343, Q9BYR6, Q9BYR7, Q9BYR8, Q9D638, Q9D7P0, A8MUX0, Q3LI83, Q4W7G7, Q4W7G8, Q4W7G9, Q6R648, Q8IUC1, A2A5X5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 69 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	19	23.0×	1e-19
Formation of the cornified envelope	9	17.2×	8e-08

GO biological processes:

GO term	Partners	Fold	FDR
keratinization	9	39.8×	4e-10

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	18
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

151 predictions. Top by Δscore:

Variant	Effect	Δscore
17:40999767:TC:T	donor_gain	0.8200
17:40999768:CC:C	donor_gain	0.8200
17:40999735:A:C	donor_gain	0.8000
17:40999768:C:CA	donor_gain	0.7900
17:40999873:G:C	donor_gain	0.7900
17:40999736:C:CC	donor_gain	0.7600
17:40999727:G:C	donor_gain	0.7100
17:40999731:CCAAA:C	donor_gain	0.7100
17:40999732:CAAAC:C	donor_gain	0.6900
17:40999877:T:A	donor_gain	0.5900
17:40999672:CAGGG:C	acceptor_gain	0.5800
17:40999765:A:AC	donor_gain	0.5800
17:40999766:C:CC	donor_gain	0.5800
17:40999729:A:T	donor_gain	0.5700
17:40999684:A:AC	acceptor_gain	0.5100
17:40999255:A:T	acceptor_gain	0.4900
17:40999730:A:C	donor_gain	0.4800
17:40999499:A:AC	donor_gain	0.4700
17:40999500:C:CC	donor_gain	0.4700
17:40999514:T:TA	donor_gain	0.4600
17:40999193:T:C	acceptor_gain	0.4500
17:40999677:C:CC	acceptor_gain	0.4500
17:40999254:CAG:C	acceptor_gain	0.4400
17:40999524:T:TA	donor_gain	0.4400
17:40999193:T:TC	acceptor_gain	0.4300
17:40999724:C:CA	donor_gain	0.4300
17:40999686:G:C	acceptor_gain	0.4200
17:40999707:G:GC	donor_gain	0.4200
17:40999734:A:T	donor_gain	0.4100
17:40999347:T:C	donor_gain	0.4000

AlphaMissense

632 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:40999656:G:C	F66L	0.978
17:40999656:G:T	F66L	0.978
17:40999658:A:G	F66L	0.978
17:40999752:G:C	S34R	0.946
17:40999752:G:T	S34R	0.946
17:40999754:T:G	S34R	0.946
17:40999657:A:C	F66C	0.925
17:40999657:A:G	F66S	0.924
17:40999748:A:G	C36R	0.924
17:40999746:G:C	C36W	0.910
17:40999651:A:T	L68H	0.882
17:40999654:A:G	L67P	0.868
17:40999740:G:C	H38Q	0.868
17:40999740:G:T	H38Q	0.868
17:40999756:G:T	P33H	0.866
17:40999761:G:C	C31W	0.865
17:40999763:A:G	C31R	0.859
17:40999661:A:G	C65R	0.855
17:40999658:A:C	F66V	0.849
17:40999654:A:T	L67Q	0.844
17:40999759:A:G	L32P	0.843
17:40999658:A:T	F66I	0.840
17:40999651:A:G	L68P	0.839
17:40999753:C:A	S34I	0.839
17:40999747:C:T	C36Y	0.837
17:40999796:A:G	C20R	0.828
17:40999757:G:T	P33T	0.827
17:40999659:G:C	C65W	0.826
17:40999794:G:C	C20W	0.826
17:40999654:A:C	L67R	0.824

dbSNP variants (sampled 300 via entrez): RS1000156375 (17:40999285 T>C), RS1000442889 (17:40999116 T>C), RS1001505919 (17:40999325 A>C), RS1001661446 (17:40999125 T>A), RS1001955823 (17:41000189 T>G), RS1002147946 (17:41001825 A>T), RS1003594536 (17:41001307 T>C), RS1004117842 (17:41000150 C>A,T), RS1004143220 (17:41001415 G>A,T), RS1004172935 (17:41001733 C>T), RS1006189089 (17:41001504 G>A,C), RS1008337861 (17:41000935 C>T), RS1010722156 (17:40999420 T>C), RS1012716180 (17:41001872 C>A,T), RS1012839427 (17:40999097 T>C)

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

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
2-methyl-4-isothiazolin-3-one	increases expression	1
beta-lapachone	decreases expression	1
CGP 52608	affects binding, increases reaction	1
Benzo(a)pyrene	increases methylation	1
Testosterone	increases expression	1

Clinical trials (associated diseases)

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