KRTAP20-3

Summary

KRTAP20-3 (keratin associated protein 20-3, HGNC:34001) is a protein-coding gene on chromosome 21q22.11, encoding Keratin-associated protein 20-3 (Q3LI60). 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 be located in intermediate filament.

Source: NCBI Gene 337985 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 7 total
• MANE Select transcript: NM_001128077

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34001
Approved symbol	KRTAP20-3
Name	keratin associated protein 20-3
Location	21q22.11
Locus type	gene with protein product
Status	Approved
Aliases	KAP20.3, KAP19D
Ensembl gene	ENSG00000206104
Ensembl biotype	protein_coding
Entrez	337985

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000382826

RefSeq mRNA: 1 — MANE Select: NM_001128077 NM_001128077

CCDS: CCDS46642

Canonical transcript exons

ENST00000382826 — 1 exons

Exon	Start	End
ENSE00001493466	30642864	30643136

Expression profiles

Bgee: expression breadth tissue_specific, 6 present calls, max score 91.48.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	91.48	gold quality
granulocyte	CL:0000094	56.55	gold quality
hindlimb stylopod muscle	UBERON:0004252	40.03	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
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	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
prefrontal cortex	UBERON:0000451	29.04	gold quality
duodenum	UBERON:0002114	28.14	gold quality
liver	UBERON:0002107	28.04	gold quality
lymph node	UBERON:0000029	27.57	gold quality
leukocyte	CL:0000738	27.36	silver 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
monocyte	CL:0000576	25.96	silver 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
muscle of leg	UBERON:0001383	24.88	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	0.98

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

9 targeting KRTAP20-3, 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-4697-3P	99.89	67.09	1123
HSA-MIR-1279	97.83	67.50	1898
HSA-MIR-1271-3P	97.56	64.85	865
HSA-MIR-550A-3-5P	97.56	65.35	823
HSA-MIR-550A-5P	97.56	65.35	823
HSA-MIR-3674	97.01	68.86	1171
HSA-MIR-711	96.60	65.75	528
HSA-MIR-4280	96.44	67.69	473
HSA-MIR-3935	96.33	66.79	797

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Keratin-associated protein 20-3 — Q3LI60 (reviewed: Q3LI60)

All UniProt accessions (1): Q3LI60

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 20 family.

RefSeq proteins (1): NP_001121549* (*=MANE)

Domains & families (InterPro)

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q3LI60-F1	41.33	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 9 (showing top): chr21q22, GOCC_INTERMEDIATE_FILAMENT_CYTOSKELETON, GOCC_SUPRAMOLECULAR_COMPLEX, GOCC_POLYMERIC_CYTOSKELETAL_FIBER, GOCC_SUPRAMOLECULAR_POLYMER, MIR3935, MIR550A_3_5P_MIR550A_5P, MIR1271_3P, MIR711

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): intermediate filament (GO:0005882)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intermediate filament cytoskeleton	1
polymeric cytoskeletal fiber	1

Protein interactions and networks

STRING

24 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KRTAP20-3	PURG	Q9UJV8	697
KRTAP20-3	GAGE2A	Q6NT46	591
KRTAP20-3	CFAP251	Q8TBY9	570
KRTAP20-3	B3GNT7	Q8NFL0	541
KRTAP20-3	ADAMTS6	Q9UKP5	474
KRTAP20-3	TM4SF1	P30408	417
KRTAP20-3	KRT17	Q04695	307
KRTAP20-3	KRTAP22-1	Q3MIV0	0
KRTAP20-3	KRTAP19-7	Q3SYF9	0
KRTAP20-3	KRTAP20-1	Q3LI63	0
KRTAP20-3	KRTAP23-1	A1A580	0
KRTAP20-3	KRTAP22-2	Q3LI68	0

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: H2A0M6, O08632, O08633, O08640, P02448, P04459, P05685, P08826, P25692, P82170, P83358, Q02957, Q02958, Q28580, Q3LHN2, Q3LI54, Q3LI58, Q3LI59, Q3LI60, Q3LI61, Q3LI63, Q3LI64, Q3LI66, Q3LI67, Q3LI68, Q3LI70, Q3LI72, Q3LI73, Q3LI77, Q3MIV0, Q3SYF9, Q4W7G7, Q4W7G8, Q4W7G9, Q4W7H0, Q4W7H1, Q6F4C6, Q6R645, Q7Z4W3, Q8C1I6

Diamond homologs: Q3LI60, Q3LI72, O08632, Q3LHN2, Q3LI70, Q3LI73, Q3SYF9, Q7Z4W3, Q8IUB9, Q925H2, Q925H7, Q925I0, Q99NG9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	6
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

113 predictions. Top by Δscore:

Variant	Effect	Δscore
21:30642894:C:G	donor_gain	0.8000
21:30642917:GAC:G	donor_gain	0.7100
21:30642934:GACT:G	donor_gain	0.7100
21:30642923:GC:G	donor_gain	0.6600
21:30642938:G:GG	donor_gain	0.6500
21:30642924:C:G	donor_gain	0.6200
21:30642922:GGC:G	donor_gain	0.6100
21:30642935:ACT:A	donor_gain	0.5900
21:30642929:GC:G	donor_gain	0.5700
21:30642930:C:G	donor_gain	0.5700
21:30642914:G:GT	donor_gain	0.5600
21:30643007:GTGGG:G	donor_gain	0.4800
21:30642903:C:T	donor_gain	0.4600
21:30642942:A:G	donor_gain	0.4500
21:30642996:A:G	donor_gain	0.4500
21:30642889:A:AG	donor_gain	0.4400
21:30642936:CT:C	donor_gain	0.4400
21:30642950:A:AG	donor_gain	0.4400
21:30643011:G:GT	donor_gain	0.4400
21:30642913:G:GT	donor_gain	0.4100
21:30642948:T:G	donor_gain	0.3900
21:30642889:A:G	donor_gain	0.3400
21:30642937:T:G	donor_gain	0.3400
21:30643008:TG:T	donor_gain	0.3400
21:30643009:GG:G	donor_gain	0.3400
21:30643010:GG:G	donor_gain	0.3400
21:30643066:C:T	donor_gain	0.3400
21:30643112:AGG:A	acceptor_gain	0.3300
21:30643113:GGG:G	acceptor_gain	0.3300
21:30642866:C:T	donor_gain	0.3200

AlphaMissense

276 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
21:30642970:T:C	F28L	0.979
21:30642972:T:A	F28L	0.979
21:30642972:T:G	F28L	0.979
21:30642961:T:C	F25L	0.955
21:30642963:T:A	F25L	0.955
21:30642963:T:G	F25L	0.955
21:30642939:T:G	C17W	0.954
21:30642997:T:C	C37R	0.928
21:30642937:T:C	C17R	0.925
21:30642937:T:A	C17S	0.921
21:30642938:G:C	C17S	0.921
21:30642997:T:A	C37S	0.921
21:30642998:G:C	C37S	0.921
21:30642987:T:G	C33W	0.908
21:30642971:T:C	F28S	0.907
21:30642999:T:G	C37W	0.907
21:30642938:G:A	C17Y	0.877
21:30642975:A:C	R29S	0.861
21:30642975:A:T	R29S	0.861
21:30643003:T:C	C39R	0.857
21:30642985:T:C	C33R	0.854
21:30642970:T:A	F28I	0.847
21:30642938:G:T	C17F	0.846
21:30642971:T:G	F28C	0.837
21:30642965:G:A	G26D	0.825
21:30643005:T:G	C39W	0.820
21:30643003:T:A	C39S	0.805
21:30643004:G:C	C39S	0.805
21:30642985:T:A	C33S	0.801
21:30642986:G:C	C33S	0.801

dbSNP variants (sampled 300 via entrez): RS1000794565 (21:30641249 T>G), RS1001076881 (21:30641658 G>A), RS1001796272 (21:30642807 G>A), RS1002378632 (21:30642458 G>A), RS1005789108 (21:30643595 A>G), RS1006137672 (21:30641968 C>T), RS1007307134 (21:30641465 T>C), RS1008310872 (21:30641683 C>A,G), RS1009207062 (21:30642228 G>T), RS1009215218 (21:30643406 G>A), RS1009266208 (21:30643185 C>A,T), RS1010181652 (21:30641168 G>A), RS1012500003 (21:30641229 C>T), RS1012913155 (21:30640983 G>T), RS1013511998 (21:30642325 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

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, increases methylation	1
pentanal	increases expression	1
Fulvestrant	increases methylation, affects cotreatment	1
Benzo(a)pyrene	affects methylation	1

Clinical trials (associated diseases)

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