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Atlas / Gene / KRT31

KRT31

gene
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Also known as Ha-1

Summary

KRT31 (keratin 31, HGNC:6448) is a protein-coding gene on chromosome 17q21.2, encoding Keratin, type I cuticular Ha1 (Q15323).

The protein encoded by this gene is a member of the keratin gene family. As a type I hair keratin, it is an acidic protein which heterodimerizes with type II keratins to form hair and nails. The type I hair keratins are clustered in a region of chromosome 17q12-q21 and have the same direction of transcription.

Source: NCBI Gene 3881 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 60 total
  • MANE Select transcript: NM_002277

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6448
Approved symbolKRT31
Namekeratin 31
Location17q21.2
Locus typegene with protein product
StatusApproved
AliasesHa-1
Ensembl geneENSG00000094796
Ensembl biotypeprotein_coding
OMIM601077
Entrez3881

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000251645

RefSeq mRNA: 1 — MANE Select: NM_002277 NM_002277

CCDS: CCDS11391

Canonical transcript exons

ENST00000251645 — 7 exons

ExonStartEnd
ENSE000008634754139719241397608
ENSE000019299704139372141394169
ENSE000023283394139642041396576
ENSE000023594054139484841395068
ENSE000023703734139546241395623
ENSE000023880404139524541395370
ENSE000024290884139691341396995

Expression profiles

Bgee: expression breadth ubiquitous, 101 present calls, max score 88.85.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1270 / max 84.5845, expressed in 12 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1658970.122211
1658960.00484

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cerebellumUBERON:000203788.85gold quality
cerebellar cortexUBERON:000212988.81gold quality
cerebellar hemisphereUBERON:000224588.80gold quality
right hemisphere of cerebellumUBERON:001489087.70gold quality
skin of abdomenUBERON:000141685.82gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047385.77gold quality
zone of skinUBERON:000001485.40gold quality
skin of legUBERON:000151185.12gold quality
cortical plateUBERON:000534382.20gold quality
hindlimb stylopod muscleUBERON:000425277.34gold quality
esophagus mucosaUBERON:000246975.45gold quality
lower esophagus mucosaUBERON:003583475.26gold quality
muscle of legUBERON:000138368.13gold quality
anterior cingulate cortexUBERON:000983567.62gold quality
gastrocnemiusUBERON:000138867.31gold quality
skeletal muscle tissueUBERON:000113464.51gold quality
prefrontal cortexUBERON:000045163.51gold quality
frontal cortexUBERON:000187060.99gold quality
Brodmann (1909) area 9UBERON:001354059.33gold quality
dorsolateral prefrontal cortexUBERON:000983459.02gold quality
superior frontal gyrusUBERON:000266158.21gold quality
cerebral cortexUBERON:000095658.19gold quality
right frontal lobeUBERON:000281057.11gold quality
esophagusUBERON:000104356.12gold quality
muscle tissueUBERON:000238555.09gold quality
vaginaUBERON:000099652.94gold quality
brainUBERON:000095552.55gold quality
primary visual cortexUBERON:000243652.10gold quality
right lungUBERON:000216751.38gold quality
ganglionic eminenceUBERON:000402349.06gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes3.71

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting KRT31, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4533100.0069.482758
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-651-3P99.9473.485177
HSA-MIR-509399.6769.262291
HSA-MIR-516B-5P99.5666.331495
HSA-MIR-448099.4266.02735
HSA-MIR-3145-3P98.8569.072031
HSA-MIR-655-5P98.7465.93888
HSA-MIR-330-5P98.7367.631788
HSA-MIR-426698.5367.291035
HSA-MIR-518C-5P98.5369.201640
HSA-MIR-32698.2566.441565
HSA-MIR-6736-5P98.1766.43760
HSA-MIR-126298.1766.52757
HSA-MIR-4701-3P98.1766.25788
HSA-MIR-443897.9663.70947
HSA-MIR-192-3P97.5267.661001
HSA-MIR-6772-3P97.0465.89784
HSA-MIR-426894.4564.09819

Literature-anchored findings (GeneRIF, showing 2)

  • the co-expression of LEF1 and beta-catenin, which in the hair follicle may initiate cortex cell differentiation through the induction of hair keratin hHa1 expression is not preserved in upper transitional cells of pilomatricomas. (PMID:15140206)
  • K31 as a novel marker for clear secretory cells in human eccrine sweat glands. (PMID:31975318)

Cross-species orthologs

0 orthologs

Paralogs (68): KRT33A (ENSG00000006059), VIM (ENSG00000026025), 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), KRT13 (ENSG00000171401)

Protein

Protein identifiers

Keratin, type I cuticular Ha1 — Q15323 (reviewed: Q15323)

Alternative names: Hair keratin, type I Ha1, Keratin-31

All UniProt accessions (1): Q15323

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Present in scalp but not in hairless skin. Abundantly expressed in the differentiating cortex of growing (anagen) hair. Expression is restricted to the keratinocytes of the hair cortex and is absent from inner root sheath and medulla.

Miscellaneous. There are two types of hair/microfibrillar keratin, I (acidic) and II (neutral to basic).

Similarity. Belongs to the intermediate filament family.

RefSeq proteins (1): NP_002268* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002957Keratin_IFamily
IPR018039IF_conservedConserved_site
IPR039008IF_rod_domDomain

Pfam: PF00038

UniProt features (14 total): region of interest 7, sequence variant 3, chain 1, domain 1, sequence conflict 1, site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q15323-F179.810.61

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): 305 (stutter)

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

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

MSigDB gene sets: 88 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_UP, GOBP_MORPHOGENESIS_OF_AN_EPITHELIUM, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_INTERMEDIATE_FILAMENT_BASED_PROCESS, GOBP_INTERMEDIATE_FILAMENT_ORGANIZATION, JAEGER_METASTASIS_DN, MODULE_45, MODULE_16, GCM_RING1, MARTINEZ_RB1_TARGETS_DN, MODULE_157, TGACATY_UNKNOWN, GOBP_EPIDERMIS_DEVELOPMENT, MODULE_88, TANAKA_METHYLATED_IN_ESOPHAGEAL_CARCINOMA

GO Biological Process (4): morphogenesis of an epithelium (GO:0002009), epidermis development (GO:0008544), epithelial cell differentiation (GO:0030855), intermediate filament organization (GO:0045109)

GO Molecular Function (4): structural constituent of cytoskeleton (GO:0005200), structural constituent of skin epidermis (GO:0030280), structural molecule activity (GO:0005198), protein binding (GO:0005515)

GO Cellular Component (6): obsolete extracellular space (GO:0005615), cytosol (GO:0005829), cytoskeleton (GO:0005856), intermediate filament (GO:0005882), keratin filament (GO:0045095), extracellular exosome (GO:0070062)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Developmental Biology1
Keratinization1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
epithelium development2
structural molecule activity2
tissue morphogenesis1
tissue development1
cell differentiation1
intermediate filament cytoskeleton organization1
supramolecular fiber organization1
cytoskeleton1
cytoskeleton organization1
molecular_function1
binding1
cytoplasm1
cellular anatomical structure1
intracellular membraneless organelle1
intermediate filament cytoskeleton1
polymeric cytoskeletal fiber1
intermediate filament1
extracellular vesicle1

Protein interactions and networks

STRING

1606 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
KRT31KRTAP3-2Q9BYR7498
KRT31LEF1Q9UJU2486
KRT31KLKB1P03952472
KRT31KRTAP3-3Q9BYR6416
KRT31KRTAP3-1Q9BYR8387
KRT31HOXC13P31276386
KRT31S100A3P33764372
KRT31OR1J1Q8NGS3367
KRT31DSG4Q86SJ6362
KRT31LCE6AA0A183355
KRT31ATAD1Q8NBU5354
KRT31KRTAP4-3Q9BYR4351
KRT31TCHHQ07283349
KRT31KRTAP19-7Q3SYF9348
KRT31OR2D2Q9H210348

IntAct

1412 interactions, top by confidence:

ABTypeScore
KRT31KRT6Apsi-mi:“MI:0915”(physical association)0.830
KRT6AKRT31psi-mi:“MI:0915”(physical association)0.830
KRT31KRT2psi-mi:“MI:0915”(physical association)0.810
KRT31HGSpsi-mi:“MI:0915”(physical association)0.780
KRT31TXLNApsi-mi:“MI:0915”(physical association)0.780
HOXA1KRT31psi-mi:“MI:0915”(physical association)0.780
KRT31INPP5Kpsi-mi:“MI:0915”(physical association)0.780
KRT31KLC4psi-mi:“MI:0915”(physical association)0.780
HGSKRT31psi-mi:“MI:0915”(physical association)0.780
KRT31GPS2psi-mi:“MI:0915”(physical association)0.740
P2RX7KRT31psi-mi:“MI:0915”(physical association)0.720
MAPKBP1KRT31psi-mi:“MI:0915”(physical association)0.720
KRT31ASMTLpsi-mi:“MI:0915”(physical association)0.720
KRT31AGR2psi-mi:“MI:0915”(physical association)0.720
KRT31KRT6Bpsi-mi:“MI:0915”(physical association)0.720
KRT31KRT8psi-mi:“MI:0915”(physical association)0.720
KRT31GSTP1psi-mi:“MI:0915”(physical association)0.720
KRT31KRT5psi-mi:“MI:0915”(physical association)0.720
KRT31PRF1psi-mi:“MI:0915”(physical association)0.720
CD33KRT31psi-mi:“MI:0915”(physical association)0.720
CCNCKRT31psi-mi:“MI:0915”(physical association)0.720
KRT31BTCpsi-mi:“MI:0915”(physical association)0.720
KRT31CDKN1Apsi-mi:“MI:0915”(physical association)0.720
KRT31NPBWR2psi-mi:“MI:0915”(physical association)0.720
KRT31KRT6Cpsi-mi:“MI:0915”(physical association)0.720
KRT31SMCPpsi-mi:“MI:0915”(physical association)0.720
KRT31GEMpsi-mi:“MI:0915”(physical association)0.720
LMO4KRT31psi-mi:“MI:0915”(physical association)0.720
KRT31KRT83psi-mi:“MI:0915”(physical association)0.720
CDK18KRT31psi-mi:“MI:0915”(physical association)0.720

BioGRID (589): KRT31 (Two-hybrid), KRT31 (Two-hybrid), KRT31 (Two-hybrid), KRT31 (Two-hybrid), KRT31 (Two-hybrid), KRT31 (Two-hybrid), KRT31 (Two-hybrid), KRT31 (Two-hybrid), KRT31 (Two-hybrid), KRT31 (Two-hybrid), KRT31 (Two-hybrid), KRT31 (Two-hybrid), KRT31 (Two-hybrid), KRT31 (Two-hybrid), KRT31 (Two-hybrid)

ESM2 similar proteins: A4FUZ0, A5A6M5, A5A6P3, A6QNX5, A7YWK3, B0LKP1, B1AQ75, E1AB55, O43790, O76009, O76013, P02534, P15241, P19013, P25690, P25691, P78385, P78386, P97861, Q0P5J7, Q14525, Q14532, Q14533, Q148H4, Q148H5, Q148H7, Q148H8, Q14CN4, Q15323, Q3SY84, Q497I4, Q61765, Q61897, Q62168, Q6IG03, Q6IG04, Q6IME9, Q6IMF0, Q6NXH9, Q86Y46

Diamond homologs: A1KQY9, A1L317, A1L595, A5A6M0, A5A6M5, A5A6N2, A5A6P3, A6BLY7, A6QQQ9, A7YWM2, B0LKP1, B1AQ75, O57607, O57611, O76009, O76013, O77727, O93256, P02533, P02534, P02535, P02537, P05781, P05783, P05784, P06394, P08727, P08728, P08730, P08777, P08778, P08779, P08802, P13645, P13646, P19001, P19012, P25030, P25690, P35527

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 174 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:

PathwayPartnersFoldFDR
Formation of the cornified envelope129.8×2e-06
Keratinization126.2×1e-04

GO biological processes:

GO termPartnersFoldFDR
keratinization1117.8×2e-08
intermediate filament organization1016.6×2e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance53
Likely benign5
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

530 predictions. Top by Δscore:

VariantEffectΔscore
17:41394840:GTACT:Gdonor_loss1.0000
17:41394843:CTCA:Cdonor_gain1.0000
17:41394844:TCA:Tdonor_loss1.0000
17:41394845:CAC:Cdonor_loss1.0000
17:41394846:A:ACdonor_gain1.0000
17:41394847:C:CCdonor_gain1.0000
17:41394847:CT:Cdonor_gain1.0000
17:41394847:CTTG:Cdonor_gain1.0000
17:41395064:TCTCG:Tacceptor_gain1.0000
17:41395065:CTCG:Cacceptor_gain1.0000
17:41395065:CTCGC:Cacceptor_gain1.0000
17:41395066:TCG:Tacceptor_gain1.0000
17:41395066:TCGCT:Tacceptor_gain1.0000
17:41395067:CG:Cacceptor_gain1.0000
17:41395067:CGC:Cacceptor_gain1.0000
17:41395069:C:CCacceptor_gain1.0000
17:41395070:T:Aacceptor_loss1.0000
17:41395071:G:Cacceptor_gain1.0000
17:41395071:G:GCacceptor_gain1.0000
17:41395074:G:Cacceptor_gain1.0000
17:41395074:G:GCacceptor_gain1.0000
17:41395241:ACACC:Adonor_loss1.0000
17:41395242:CA:Cdonor_loss1.0000
17:41395243:ACCAG:Adonor_loss1.0000
17:41395366:TCGGT:Tacceptor_gain1.0000
17:41395367:CGGT:Cacceptor_gain1.0000
17:41395367:CGGTC:Cacceptor_gain1.0000
17:41395368:GGT:Gacceptor_gain1.0000
17:41395369:GT:Gacceptor_gain1.0000
17:41395370:TC:Tacceptor_loss1.0000

AlphaMissense

2718 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:41395264:A:GL286P0.997
17:41397343:C:GR66P0.997
17:41395259:C:GA288P0.995
17:41397340:A:GL67P0.995
17:41394971:A:GL325P0.994
17:41395013:A:GL311P0.994
17:41395297:A:GL275P0.994
17:41396944:C:GA134P0.994
17:41394887:A:GI353T0.993
17:41396502:A:GL169P0.993
17:41397202:A:GL113P0.993
17:41397310:A:GL77P0.993
17:41394899:A:GL349P0.992
17:41394959:C:GR329P0.992
17:41395291:C:GR277P0.992
17:41396481:A:GL176P0.992
17:41394887:A:CI353S0.991
17:41394920:A:GL342P0.991
17:41395046:A:GL300P0.991
17:41395246:A:GL292P0.991
17:41395276:A:GL282P0.991
17:41395360:A:GL254P0.991
17:41396460:A:GL183P0.991
17:41394944:C:GR334P0.990
17:41395471:G:CF247L0.990
17:41395471:G:TF247L0.990
17:41395473:A:GF247L0.990
17:41395538:A:GL225P0.990
17:41397340:A:TL67Q0.990
17:41394875:C:GR357P0.989

dbSNP variants (sampled 300 via entrez): RS1000113340 (17:41397315 A>T), RS1001526131 (17:41397739 C>T), RS1001777836 (17:41398587 G>A), RS1001923688 (17:41396203 G>C), RS1002597644 (17:41398624 A>T), RS1002934303 (17:41398901 ATATATATATATTTTT>A), RS1003716425 (17:41393509 G>A), RS1004248566 (17:41393938 C>G), RS1004260043 (17:41394099 A>T), RS1004481883 (17:41393295 A>G), RS1004586037 (17:41395068 G>A,C), RS1004810996 (17:41393466 G>T), RS1005831599 (17:41398379 T>C,G), RS1005883883 (17:41398583 T>C), RS1006598138 (17:41397960 G>T)

Disease associations

OMIM: gene MIM:601077 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

StudyTraitp-value
GCST006989_5Brown vs. black hair color1.000000e-09

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0003924hair color

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects cotreatment, decreases expression, increases expression2
bisphenol Faffects cotreatment, decreases expression1
2-bromopalmitatedecreases reaction, increases abundance, increases palmitoylation1
CGP 52608affects binding, increases reaction1
Leflunomideincreases expression1
Air Pollutantsdecreases expression1
Atrazineincreases expression1
Benzo(a)pyreneincreases methylation1
Cadmiumdecreases reaction, increases abundance, increases palmitoylation1
Carmustinedecreases expression1
Dexamethasoneaffects cotreatment, decreases expression1
Diethylhexyl Phthalatedecreases expression1
Indomethacinaffects cotreatment, decreases expression1
Phenolsulfonphthaleinaffects cotreatment, increases expression1
Rotenonedecreases expression1
Tetrachlorodibenzodioxinincreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, decreases expression1
Cadmium Chloridedecreases reaction, increases abundance, increases palmitoylation1
beta-Naphthoflavoneincreases expression1
Lactic Aciddecreases expression1

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.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 75

This page pulls from 75 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomereactomeparentrefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot