KRT79

Summary

KRT79 (keratin 79, HGNC:28930) is a protein-coding gene on chromosome 12q13.13, encoding Keratin, type II cytoskeletal 79 (Q5XKE5).

Keratins are intermediate filament proteins responsible for the structural integrity of epithelial cells and are subdivided into epithelial keratins and hair keratins. This gene encodes an epithelial keratin that is expressed in skeletal muscle, skin and scalp. The type II keratins are clustered in a region of chromosome 12q13.

Source: NCBI Gene 338785 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 85 total
• MANE Select transcript: NM_175834

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28930
Approved symbol	KRT79
Name	keratin 79
Location	12q13.13
Locus type	gene with protein product
Status	Approved
Aliases	K6L, KRT6L
Ensembl gene	ENSG00000185640
Ensembl biotype	protein_coding
OMIM	611160
Entrez	338785

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 retained_intron

ENST00000330553, ENST00000546453, ENST00000549255

RefSeq mRNA: 1 — MANE Select: NM_175834 NM_175834

CCDS: CCDS8839

Canonical transcript exons

ENST00000330553 — 9 exons

Exon	Start	End
ENSE00001294512	52833784	52834311
ENSE00001316897	52831406	52831626
ENSE00001320287	52821408	52822077
ENSE00001655792	52830232	52830292
ENSE00003492011	52824198	52824362
ENSE00003537050	52823016	52823236
ENSE00003554597	52823887	52824012
ENSE00003609849	52830023	52830118
ENSE00003670411	52822345	52822379

Expression profiles

Bgee: expression breadth broad, 82 present calls, max score 95.51.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.5859 / max 414.3116, expressed in 92 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
131159	1.3791	26
131161	0.1122	19
131160	0.0946	55

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
upper leg skin	UBERON:0004262	95.51	gold quality
mammalian vulva	UBERON:0000997	92.83	gold quality
skin of abdomen	UBERON:0001416	81.32	gold quality
zone of skin	UBERON:0000014	79.07	gold quality
lower esophagus mucosa	UBERON:0035834	78.06	gold quality
skin of leg	UBERON:0001511	77.69	gold quality
nipple	UBERON:0002030	76.34	gold quality
biceps brachii	UBERON:0001507	67.32	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	65.93	gold quality
secondary oocyte	CL:0000655	64.65	gold quality
esophagus mucosa	UBERON:0002469	63.48	gold quality
nasal cavity epithelium	UBERON:0005384	63.17	gold quality
heart right ventricle	UBERON:0002080	57.72	gold quality
pigmented layer of retina	UBERON:0001782	56.37	gold quality
decidua	UBERON:0002450	56.37	gold quality
esophagus squamous epithelium	UBERON:0006920	56.37	gold quality
postcentral gyrus	UBERON:0002581	56.20	gold quality
subcutaneous adipose tissue	UBERON:0002190	56.17	gold quality
adipose tissue	UBERON:0001013	56.03	gold quality
entorhinal cortex	UBERON:0002728	55.79	gold quality
buccal mucosa cell	CL:0002336	55.40	gold quality
mammary duct	UBERON:0001765	54.68	gold quality
omental fat pad	UBERON:0010414	54.47	gold quality
peritoneum	UBERON:0002358	54.43	gold quality
adipose tissue of abdominal region	UBERON:0007808	54.42	gold quality
colonic mucosa	UBERON:0000317	54.31	gold quality
parotid gland	UBERON:0001831	54.13	gold quality
mucosa of sigmoid colon	UBERON:0004993	53.65	gold quality
parietal lobe	UBERON:0001872	53.42	gold quality
jejunum	UBERON:0002115	53.39	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.13

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): IRF1, STAT1

miRNA regulators (miRDB)

23 targeting KRT79, 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-7110-3P	100.00	73.18	2486
HSA-MIR-6759-5P	99.99	66.54	785
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-4525	99.94	64.38	675
HSA-MIR-5010-5P	99.94	64.11	705
HSA-MIR-6817-3P	99.79	68.35	2126
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-4763-3P	99.10	67.83	2649
HSA-MIR-1286	99.09	66.23	1046
HSA-MIR-4324	99.04	70.14	1569
HSA-MIR-4270	99.02	66.26	1987
HSA-MIR-6769B-5P	98.73	64.91	1092
HSA-MIR-6864-5P	98.38	66.59	1079
HSA-MIR-211-3P	98.14	66.77	1052
HSA-MIR-3132	97.96	67.91	711
HSA-MIR-197-5P	97.23	68.10	596
HSA-MIR-12128	96.67	66.98	1471
HSA-MIR-4774-5P	95.92	68.27	827
HSA-MIR-6879-3P	93.93	64.00	759

Literature-anchored findings (GeneRIF, showing 1)

• migratory keratinocytes express keratin 79 and stream out of the hair germ and into the epidermis prior to lumen formation in the embryo. (PMID:24198274)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Krt79	ENSMUSG00000061397
rattus_norvegicus	Krt79	ENSRNOG00000058340

Paralogs (68): KRT33A (ENSG00000006059), VIM (ENSG00000026025), KRT31 (ENSG00000094796), NEFM (ENSG00000104722), KRT23 (ENSG00000108244), KRT37 (ENSG00000108417), KRT32 (ENSG00000108759), KRT18 (ENSG00000111057), LMNB1 (ENSG00000113368), KRT36 (ENSG00000126337), KRT17 (ENSG00000128422), GFAP (ENSG00000131095), KRT34 (ENSG00000131737), KRT33B (ENSG00000131738), NES (ENSG00000132688), PRPH (ENSG00000135406), KRT85 (ENSG00000135443), KRT7 (ENSG00000135480), KRT71 (ENSG00000139648), INA (ENSG00000148798), LMNTD1 (ENSG00000152936), LMNA (ENSG00000160789), KRT84 (ENSG00000161849), KRT82 (ENSG00000161850), KRT80 (ENSG00000167767), KRT1 (ENSG00000167768), KRT24 (ENSG00000167916), KRT8 (ENSG00000170421), KRT78 (ENSG00000170423), KRT86 (ENSG00000170442), KRT75 (ENSG00000170454), KRT6C (ENSG00000170465), KRT4 (ENSG00000170477), KRT74 (ENSG00000170484), KRT72 (ENSG00000170486), KRT83 (ENSG00000170523), BFSP2 (ENSG00000170819), KRT19 (ENSG00000171345), KRT15 (ENSG00000171346), KRT38 (ENSG00000171360)

Protein

Protein identifiers

Keratin, type II cytoskeletal 79 — Q5XKE5 (reviewed: Q5XKE5)

Alternative names: Cytokeratin-79, Keratin-6-like, Keratin-79, Type-II keratin Kb38

All UniProt accessions (2): Q5XKE5, H0YID6

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Heterotetramer of two type I and two type II keratins.

Tissue specificity. Expressed in skeletal muscle, skin and scalp, but not in any other tissues or organs examined.

Miscellaneous. There are two types of cytoskeletal and microfibrillar keratin, I (acidic) and II (neutral to basic) (40-55 and 56-70 kDa, respectively).

Similarity. Belongs to the intermediate filament family.

RefSeq proteins (1): NP_787028* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003054	Keratin_II	Family
IPR018039	IF_conserved	Conserved_site
IPR032444	Keratin_2_head	Domain
IPR039008	IF_rod_dom	Domain

Pfam: PF00038, PF16208

UniProt features (18 total): region of interest 8, sequence variant 4, compositionally biased region 3, chain 1, domain 1, site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5XKE5-F1	71.07	0.43

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 395 (stutter)

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-6805567	Keratinization
R-HSA-6809371	Formation of the cornified envelope
R-HSA-1266738	Developmental Biology

MSigDB gene sets: 53 (showing top): GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_DN, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_INTERMEDIATE_FILAMENT_BASED_PROCESS, GOBP_INTERMEDIATE_FILAMENT_ORGANIZATION, EFC_Q6, GOBP_EPIDERMAL_CELL_DIFFERENTIATION, MARTINEZ_RB1_TARGETS_UP, GOBP_EPIDERMIS_DEVELOPMENT, GOBP_KERATINIZATION, GOBP_SKIN_DEVELOPMENT, GOCC_INTERMEDIATE_FILAMENT_CYTOSKELETON, GOCC_KERATIN_FILAMENT, GOMF_STRUCTURAL_MOLECULE_ACTIVITY, MARTENS_TRETINOIN_RESPONSE_UP, WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_8D

GO Biological Process (2): keratinization (GO:0031424), intermediate filament organization (GO:0045109)

GO Molecular Function (3): enzyme binding (GO:0019899), structural constituent of skin epidermis (GO:0030280), protein binding (GO:0005515)

GO Cellular Component (4): cytosol (GO:0005829), keratin filament (GO:0045095), extracellular exosome (GO:0070062), intermediate filament (GO:0005882)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Developmental Biology	1
Keratinization	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
keratinocyte differentiation	1
multicellular organismal process	1
intermediate filament cytoskeleton organization	1
supramolecular fiber organization	1
protein binding	1
structural molecule activity	1
binding	1
cytoplasm	1
cellular anatomical structure	1
intermediate filament	1
extracellular vesicle	1
intermediate filament cytoskeleton	1
polymeric cytoskeletal fiber	1

Protein interactions and networks

STRING

831 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KRT79	LRIG1	Q96JA1	575
KRT79	PLET1	Q6UQ28	447
KRT79	GLI1	P08151	410
KRT79	LGR5	O75473	406
KRT79	CD200	P41217	406
KRT79	LRRC30	A6NM36	396
KRT79	KRTAP9-2	Q9BYQ4	380
KRT79	KRTAP1-1	Q07627	369
KRT79	KRT2	P35908	355
KRT79	CD34	P28906	353
KRT79	MMP9	P14780	350
KRT79	SPATA31A1	Q5TZJ5	348
KRT79	TLN1	Q9Y490	336
KRT79	TLN2	Q9Y4G6	333
KRT79	ATP6V1C2	Q8NEY4	308

IntAct

90 interactions, top by confidence:

A	B	Type	Score
KRT79	KRT15	psi-mi:“MI:0915”(physical association)	0.780
KRT33B	KRT79	psi-mi:“MI:0915”(physical association)	0.780
KRT15	KRT79	psi-mi:“MI:0915”(physical association)	0.780
KRT79	KRT33B	psi-mi:“MI:0915”(physical association)	0.780
KRT38	KRT79	psi-mi:“MI:0915”(physical association)	0.740
KRT79	KRT38	psi-mi:“MI:0915”(physical association)	0.740
KRT79	KRT31	psi-mi:“MI:0915”(physical association)	0.720
KRT31	KRT79	psi-mi:“MI:0915”(physical association)	0.720
KRT79	KRT27	psi-mi:“MI:0915”(physical association)	0.600
KRT79	KRT13	psi-mi:“MI:0915”(physical association)	0.560
USHBP1	KRT79	psi-mi:“MI:0915”(physical association)	0.560
KRT79	USHBP1	psi-mi:“MI:0915”(physical association)	0.560
KRT13	KRT79	psi-mi:“MI:0915”(physical association)	0.560
KRT16	KRT79	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (79): KRT79 (Two-hybrid), KRT79 (Two-hybrid), KRT79 (Two-hybrid), KRT79 (Two-hybrid), KRT79 (Two-hybrid), KRT79 (Two-hybrid), KRT79 (Affinity Capture-MS), KRT79 (Affinity Capture-MS), KRT79 (Affinity Capture-MS), KRT79 (Affinity Capture-MS), KRT79 (Affinity Capture-MS), KRT79 (Affinity Capture-MS), KRT79 (Affinity Capture-MS), KRT79 (Affinity Capture-MS), KRT79 (Affinity Capture-MS)

ESM2 similar proteins: A0JND2, A3KN27, A5A6N0, A6BLY7, A6H712, A6QNX5, A7YWK3, E1AB55, P07744, P08729, P19013, P25691, Q0P5J4, Q0P5J6, Q0P5J7, Q0VBK2, Q148H5, Q148H6, Q148H7, Q148H8, Q14CN4, Q3SY84, Q5XKE5, Q64291, Q6IFW8, Q6IFZ9, Q6IG00, Q6IG01, Q6IG03, Q6IG04, Q6IME9, Q6IMF0, Q6IMF1, Q6KB66, Q6NXH9, Q6R649, Q7RTS7, Q7Z3Y7, Q7Z3Y9, Q7Z794

Diamond homologs: A0A125S9M6, A0JND2, A4FUZ0, A5A6M8, A6NCN2, A7YWK3, O43790, P02542, P02545, P02547, P02548, P04104, P04260, P04261, P04262, P04263, P07196, P07744, P08551, P08928, P09010, P10999, P12035, P12036, P13647, P13648, P15241, P16884, P19013, P19246, P19527, P21619, P21910, P25691, P35908, P48671, P48672, P48678, P48679, P78385

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 42 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
Formation of the cornified envelope	16	48.5×	3e-22
Keratinization	16	30.7×	3e-19

GO biological processes:

GO term	Partners	Fold	FDR
morphogenesis of an epithelium	15	151.7×	3e-28
intermediate filament organization	15	106.2×	7e-26
epithelial cell differentiation	13	67.1×	2e-19

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	74
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1037 predictions. Top by Δscore:

Variant	Effect	Δscore
12:52822073:CACAG:C	acceptor_gain	1.0000
12:52822075:CAG:C	acceptor_gain	1.0000
12:52822078:C:CC	acceptor_gain	1.0000
12:52822343:A:AC	donor_gain	1.0000
12:52822344:C:CC	donor_gain	1.0000
12:52822952:C:CA	donor_gain	1.0000
12:52822985:G:C	donor_gain	1.0000
12:52823010:CACCA:C	donor_loss	1.0000
12:52823011:ACCAC:A	donor_loss	1.0000
12:52823013:CA:C	donor_loss	1.0000
12:52823014:A:C	donor_loss	1.0000
12:52823022:T:A	donor_gain	1.0000
12:52823031:T:A	donor_gain	1.0000
12:52823064:T:TA	donor_gain	1.0000
12:52823235:CA:C	acceptor_gain	1.0000
12:52823236:ACT:A	acceptor_loss	1.0000
12:52823237:C:CC	acceptor_gain	1.0000
12:52823238:T:C	acceptor_loss	1.0000
12:52823242:C:CT	acceptor_gain	1.0000
12:52823242:C:T	acceptor_gain	1.0000
12:52823243:A:T	acceptor_gain	1.0000
12:52823881:TCCCA:T	donor_loss	1.0000
12:52823882:CCCA:C	donor_loss	1.0000
12:52823883:CCA:C	donor_loss	1.0000
12:52823884:CA:C	donor_loss	1.0000
12:52823886:C:CG	donor_loss	1.0000
12:52824013:C:CC	acceptor_gain	1.0000
12:52824021:C:CT	acceptor_gain	1.0000
12:52824194:TCA:T	donor_loss	1.0000
12:52824195:CACCT:C	donor_loss	1.0000

AlphaMissense

3503 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:52833802:G:C	F153L	0.995
12:52833802:G:T	F153L	0.995
12:52833804:A:G	F153L	0.995
12:52833803:A:G	F153S	0.989
12:52833803:A:C	F153C	0.988
12:52833812:T:A	N150I	0.985
12:52831607:T:G	Q166P	0.984
12:52833811:G:C	N150K	0.984
12:52833811:G:T	N150K	0.984
12:52833815:A:G	L149P	0.981
12:52823037:A:G	L449P	0.980
12:52823043:C:G	R447P	0.980
12:52831616:A:G	L163P	0.977
12:52831622:C:G	R161P	0.975
12:52833815:A:T	L149H	0.975
12:52833800:G:T	A154D	0.974
12:52831584:A:G	W174R	0.972
12:52831584:A:T	W174R	0.972
12:52823047:A:C	Y446D	0.968
12:52823047:A:G	Y446H	0.968
12:52831585:C:A	K173N	0.968
12:52831585:C:G	K173N	0.968
12:52831610:T:G	Q165P	0.968
12:52833824:A:G	I146T	0.967
12:52823055:A:C	I443S	0.966
12:52823067:A:G	L439P	0.966
12:52823088:A:G	L432P	0.966
12:52823118:A:G	L422P	0.965
12:52833793:G:C	F156L	0.965
12:52833793:G:T	F156L	0.965

dbSNP variants (sampled 300 via entrez): RS1000099622 (12:52825840 C>A,T), RS1000245535 (12:52830835 G>A,T), RS1000255684 (12:52833934 A>C), RS1000467090 (12:52828722 C>G,T), RS1000573135 (12:52829737 C>T), RS1000582808 (12:52829434 C>T), RS1000700322 (12:52827088 C>T), RS1001124758 (12:52834601 C>G,T), RS1001199246 (12:52827348 T>C), RS1001270605 (12:52834944 G>T), RS1001466959 (12:52829894 A>C), RS1001573646 (12:52835556 C>T), RS1001806762 (12:52835157 T>A), RS1002023318 (12:52822860 G>A), RS1002043648 (12:52829055 A>G)

Disease associations

OMIM: gene MIM:611160 | 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

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
sodium arsenate	decreases expression, increases abundance	1
perfluorooctanoic acid	decreases expression	1
2,3,5-(triglutathion-S-yl)hydroquinone	decreases ADP-ribosylation	1
CGP 52608	affects binding, increases reaction	1
bisphenol B	increases expression	1
theaflavin-3,3’-digallate	affects expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	increases abundance, decreases expression	1
Benzo(a)pyrene	increases methylation	1
Thiram	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Aflatoxin B1	increases methylation	1
Copper Sulfate	decreases expression	1
Lactic Acid	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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