KRTAP3-1

gene

On this page

Also known as KAP3.1

Summary

KRTAP3-1 (keratin associated protein 3-1, HGNC:16778) is a protein-coding gene on chromosome 17q21.2, encoding Keratin-associated protein 3-1 (Q9BYR8). 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 83896 — RefSeq curated summary.

At a glance

Clinical variants (ClinVar): 22 total
MANE Select transcript: NM_031958

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16778
Approved symbol	KRTAP3-1
Name	keratin associated protein 3-1
Location	17q21.2
Locus type	gene with protein product
Status	Approved
Aliases	KAP3.1
Ensembl gene	ENSG00000212901
Ensembl biotype	protein_coding
Entrez	83896

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000391588, ENST00000581033

RefSeq mRNA: 1 — MANE Select: NM_031958 NM_031958

CCDS: CCDS32645

Canonical transcript exons

ENST00000391588 — 1 exons

Exon	Start	End
ENSE00001509367	41008521	41009128

Expression profiles

Bgee: expression breadth broad, 82 present calls, max score 51.67.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4632 / max 184.9496, expressed in 58 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
165863	0.4632	58

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
skin of abdomen	UBERON:0001416	51.67	gold quality
zone of skin	UBERON:0000014	49.75	gold quality
skin of leg	UBERON:0001511	48.70	gold quality
right lung	UBERON:0002167	44.45	gold 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
right lobe of liver	UBERON:0001114	36.04	silver quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
gastrocnemius	UBERON:0001388	35.24	gold quality
muscle of leg	UBERON:0001383	34.79	gold quality
vagina	UBERON:0000996	34.40	gold quality
blood	UBERON:0000178	33.44	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
liver	UBERON:0002107	33.34	silver quality
heart left ventricle	UBERON:0002084	32.21	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
tibial artery	UBERON:0007610	31.93	gold quality
islet of Langerhans	UBERON:0000006	31.92	gold quality
popliteal artery	UBERON:0002250	31.92	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
prostate gland	UBERON:0002367	30.60	gold quality
subcutaneous adipose tissue	UBERON:0002190	30.50	gold quality
pancreas	UBERON:0001264	30.13	gold quality
esophagus mucosa	UBERON:0002469	30.11	gold quality
right atrium auricular region	UBERON:0006631	30.03	gold quality
heart	UBERON:0000948	30.00	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.02

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

28 targeting KRTAP3-1, 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-371B-5P	99.99	75.34	4759
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-4639-5P	99.81	67.37	1028
HSA-MIR-34B-5P	99.78	67.56	1175
HSA-MIR-449C-5P	99.78	67.63	1168
HSA-MIR-2682-5P	99.73	67.38	1055
HSA-MIR-561-3P	99.64	70.90	3647
HSA-MIR-372-5P	99.41	69.11	2299
HSA-MIR-4786-3P	99.36	68.35	1390
HSA-MIR-371A-5P	99.08	66.51	1914
HSA-MIR-224-3P	98.91	68.42	1815
HSA-MIR-522-3P	98.91	68.56	1817
HSA-MIR-487A-5P	98.85	69.37	993
HSA-MIR-487B-5P	98.85	69.48	987
HSA-MIR-4477A	98.83	69.75	2952
HSA-MIR-2467-3P	98.65	67.18	1969
HSA-MIR-1263	98.13	69.18	459
HSA-MIR-6806-5P	96.37	68.74	587
HSA-MIR-5586-3P	95.51	67.00	805
HSA-MIR-3174	94.63	63.64	577
HSA-MIR-4765	93.11	66.17	737

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Krtap3-1	ENSMUSG00000047564
rattus_norvegicus	Krtap3-1	ENSRNOG00000012544

Paralogs (3): KRTAP24-1 (ENSG00000188694), KRTAP3-3 (ENSG00000212899), KRTAP3-2 (ENSG00000212900)

Protein

Protein identifiers

Keratin-associated protein 3-1 — Q9BYR8 (reviewed: Q9BYR8)

Alternative names: High sulfur keratin-associated protein 3.1, Keratin-associated protein 3.1

All UniProt accessions (1): Q9BYR8

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_114164* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007659	Keratin_matx	Family

Pfam: PF04579

UniProt features (6 total): repeat 4, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BYR8-F1	42.36	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: 55 (showing top): MARTINEZ_RB1_TARGETS_DN, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOCC_INTERMEDIATE_FILAMENT_CYTOSKELETON, GOCC_KERATIN_FILAMENT, GOMF_STRUCTURAL_MOLECULE_ACTIVITY, GOCC_SUPRAMOLECULAR_COMPLEX, GOCC_POLYMERIC_CYTOSKELETAL_FIBER, WNT_UP.V1_DN, REACTOME_KERATINIZATION, GOCC_SUPRAMOLECULAR_POLYMER, GREB1_TARGET_GENES, HHEX_TARGET_GENES, HMG20B_TARGET_GENES, LHX9_TARGET_GENES, NKX2_3_TARGET_GENES

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

418 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KRTAP3-1	KRTAP11-1	Q8IUC1	716
KRTAP3-1	KRTAP13-1	Q8IUC0	685
KRTAP3-1	KRTAP15-1	Q3LI76	666
KRTAP3-1	KRTAP9-3	Q9BYQ3	587
KRTAP3-1	KRTAP9-4	Q9BYQ2	576
KRTAP3-1	KRTAP4-3	Q9BYR4	570
KRTAP3-1	KRTAP13-3	Q3SY46	567
KRTAP3-1	KRT35	Q92764	543
KRTAP3-1	KRT27	Q7Z3Y8	535
KRTAP3-1	KRT80	Q6KB66	530
KRTAP3-1	KRT38	O76015	520
KRTAP3-1	KRT84	Q9NSB2	520
KRTAP3-1	KRTAP4-1	Q9BYQ7	519
KRTAP3-1	KRTAP24-1	Q3LI83	505
KRTAP3-1	KRT36	O76013	504

IntAct

270 interactions, top by confidence:

A	B	Type	Score
KRTAP3-1	NOTCH2NLA	psi-mi:“MI:0915”(physical association)	0.560
CFP	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560
CDKN1A	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560
ADAM12	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560
CERK	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560
KRTAP9-3	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560
KRTAP3-1	MRPL40	psi-mi:“MI:0915”(physical association)	0.560
TEKT3	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560
KRTAP3-1	DMRT3	psi-mi:“MI:0915”(physical association)	0.560
DOCK2	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560
KRTAP3-1	CIMIP1	psi-mi:“MI:0915”(physical association)	0.560
KRTAP3-1	PLSCR4	psi-mi:“MI:0915”(physical association)	0.560
LRRC41	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560
FAM222B	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560
SAMD7	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560
GSTP1	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560
POLR1C	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560
PVR	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560
VENTX	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560
KRTAP3-1	GNE	psi-mi:“MI:0915”(physical association)	0.560
OTX1	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560
WDR25	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560
KRTAP6-1	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-8	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560
LCE3D	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560
AGXT	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560
MAPKBP1	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560
CYSRT1	KRTAP3-1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (84): NOTCH2NL (Two-hybrid), KRTAP3-1 (Two-hybrid), KRTAP3-1 (Two-hybrid), KRTAP3-1 (Two-hybrid), KRTAP3-1 (Two-hybrid), KRTAP3-1 (Two-hybrid), KRTAP3-1 (Two-hybrid), KRTAP3-1 (Two-hybrid), KRTAP3-1 (Two-hybrid), KRTAP3-1 (Two-hybrid), KRTAP3-1 (Two-hybrid), KRTAP3-1 (Two-hybrid), KRTAP3-1 (Two-hybrid), KRTAP3-1 (Two-hybrid), KRTAP3-1 (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, A2A5X5, A8MUX0, Q8IUC1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 81 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	15	18.2×	3e-13
Formation of the cornified envelope	6	11.5×	1e-03

GO biological processes:

GO term	Partners	Fold	FDR
keratinization	7	23.4×	1e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	19
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

190 predictions. Top by Δscore:

Variant	Effect	Δscore
17:41008957:T:C	donor_gain	0.8500
17:41008686:AG:A	donor_gain	0.7400
17:41008841:A:AC	donor_gain	0.7200
17:41008842:C:CC	donor_gain	0.7200
17:41008847:T:TA	donor_gain	0.7100
17:41008837:T:TA	donor_gain	0.6900
17:41008845:AGT:A	donor_gain	0.6900
17:41008879:A:T	acceptor_gain	0.6800
17:41008845:A:AC	donor_gain	0.6600
17:41008928:G:GC	donor_gain	0.6600
17:41009007:T:C	donor_gain	0.6600
17:41008907:G:A	donor_gain	0.6500
17:41008989:C:CA	donor_gain	0.6400
17:41008845:AGTC:A	donor_gain	0.6100
17:41009000:G:C	donor_gain	0.6100
17:41008823:G:C	donor_gain	0.6000
17:41008822:A:AC	donor_gain	0.5800
17:41008894:A:AC	donor_gain	0.5800
17:41008988:TC:T	donor_gain	0.5800
17:41008989:CC:C	donor_gain	0.5800
17:41008895:G:C	donor_gain	0.5700
17:41008846:G:C	donor_gain	0.5500
17:41008803:T:A	donor_gain	0.5400
17:41008805:A:AC	donor_gain	0.5200
17:41008806:C:CC	donor_gain	0.5200
17:41008905:T:C	acceptor_gain	0.5200
17:41008805:ACAG:A	donor_gain	0.5100
17:41008806:CAGC:C	donor_gain	0.5100
17:41008818:A:C	donor_gain	0.5100
17:41008687:G:C	donor_gain	0.5000

AlphaMissense

635 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:41008879:A:G	W66R	0.884
17:41008879:A:T	W66R	0.884
17:41008877:C:A	W66C	0.876
17:41008877:C:G	W66C	0.876
17:41008973:G:C	S34R	0.830
17:41008973:G:T	S34R	0.830
17:41008975:T:G	S34R	0.830
17:41008836:A:G	I80T	0.817
17:41008836:A:C	I80S	0.765
17:41008875:A:G	L67P	0.747
17:41008872:A:T	L68H	0.722
17:41008967:G:C	C36W	0.717
17:41008969:A:G	C36R	0.705
17:41008824:G:A	T84I	0.703
17:41008878:C:A	W66L	0.693
17:41008879:A:C	W66G	0.669
17:41008880:G:C	C65W	0.664
17:41008934:G:C	C47W	0.661
17:41008884:G:A	T64I	0.657
17:41008982:G:C	C31W	0.651
17:41008961:A:C	H38Q	0.643
17:41008961:A:T	H38Q	0.643
17:41008872:A:G	L68P	0.637
17:41008947:A:T	L43H	0.636
17:41008974:C:A	S34I	0.625
17:41008882:A:G	C65R	0.617
17:41008977:G:T	P33H	0.617
17:41008878:C:G	W66S	0.610
17:41008931:A:C	C48W	0.607
17:41008875:A:T	L67Q	0.602

dbSNP variants (sampled 300 via entrez): RS1001168680 (17:41010385 C>G), RS1003639073 (17:41008553 T>C), RS1005981675 (17:41009523 A>G), RS1009681123 (17:41009391 T>C), RS1009774670 (17:41010321 T>G), RS1009985478 (17:41010410 C>T), RS1010425802 (17:41010864 C>T), RS1012227010 (17:41008620 G>T), RS1012556483 (17:41009816 A>C), RS1013886716 (17:41009858 A>G), RS1016086467 (17:41009541 T>C), RS1017077610 (17:41008022 G>A), RS1017151536 (17:41008332 A>G,T), RS1017414560 (17:41009423 C>A,T), RS1017550242 (17:41009125 C>G,T)

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

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases methylation, increases expression	5
Estradiol	affects expression, decreases expression	3
Tetrachlorodibenzodioxin	increases expression	2
Aflatoxin B1	increases expression	2
OTX015	decreases expression	1
mivebresib	decreases expression	1
bisphenol A	affects cotreatment, decreases methylation	1
tris(2-butoxyethyl) phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	decreases expression	1
tebuconazole	decreases expression	1
cylindrospermopsin	increases expression	1
(+)-JQ1 compound	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Camptothecin	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Silver	increases expression	1
Urethane	decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.