Chromosome 3

Chromosome 3 is one of the 23 pairs of chromosomes in humans. 

People normally have two copies of this chromosome. 

Chromosome 3 spans 201 million base pairs and represents about 6.5 percent of the total DNA in cells.

The following is a partial list of genes on human chromosome 3.

Partial list of the genes located on p-arm (short arm) of human chromosome 3:

ALAS1: aminolevulinate, delta-, synthase 1

APEH: encoding enzyme Acylamino-acid-releasing enzyme

ARPP-21: Cyclic AMP-regulated phosphoprotein, 21 kDa

AZI2: encoding protein 5-azacytidine-induced protein 2

BRK1: SCAR/WAVE actin nucleating complex subunit

BRPF1: bromodomain and PHD finger containing 1

BTD: biotinidase

C3orf14-Chromosome 3 open reading frame 14: predicted DNA binding protein.

CFAP20DC: encoding protein Chromosome 3 open reading frame 67

C3orf62: chromosome 3 open reading frame 62

CACNA2D3: calcium channel, voltage-dependent, alpha 2/delta subunit 3

CCR5: chemokine (C-C motif) receptor 5

CGGBP1: CGG triplet repeat binding protein 1

CMTM7: CKLF like MARVEL transmembrane domain containing 7

CNTN4: Contactin 4

COL7A1: Collagen, type VII, alpha 1 (epidermolysis bullosa, dystrophic, dominant and recessive)

CRBN: Cereblon protein[11]

DCLK3: Doublecortin like kinase 3

DLEC1: encoding protein Deleted in lung and esophageal cancer 1

EAF1: ELL associated factor 1

ENTPD3: ectonucleoside triphosphate diphosphohydrolase 3

FAM107A: Family with sequence similarity 107 member A

FAM19A1: Family with sequence similarity 19 member A1, C-C motif chemokine like

FBXL2: F-box and leucine rich repeat protein 2

FOXP1: Forkhead Box Protein P1

FRA3A encoding protein Fragile site, aphidicolin type, common, fra(3)(p24.2)

FRMD4B encoding protein FERM domain containing 4B

GHRLOS: non-coding RNA ghrelin opposite strand (non-protein coding)

GMPPB: GDP-mannose pyrophosphorylase B

HACL1: encoding protein 2-hydroxyacyl-CoA lyase 1

HEMK1: encoding protein HemK methyltransferase family member 1

HIGD1A: HIG1 domain family member 1A

HTD2: encoding protein Hydroxyacyl-thioester dehydratase type 2

LARS2: leucyl-tRNA synthetase, mitochondrial

LIMD1: LIM domain-containing protein 1

LOC105377021: encoding protein LOC105377021

LINC00312: Long intergenic non-protein-coding RNA 312

LZTFL1: Leucine zipper transcription factor like 1

MIR138-1: encoding protein MicroRNA 138-1

MIR885: encoding protein MicroRNA 885

MITF: microphthalmia-associated transcription factor

MLH1: mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)

MYRIP: Myosin VIIA and Rab interacting protein

NBEAL2: Neurobeachin-like 2

NDUFAF3: encoding enzyme NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 3

NKTR: NK-tumor recognition protein

NPRL2: Nitrogen permease regulator 2-like protein

OXTR: oxytocin receptor

PCAF: acetyltransferase activity

PHF7 encoding protein PHD finger protein 7

PRICKLE2: encoding protein Prickle planar cell polarity protein 2

PTHR1: parathyroid hormone receptor 1

QRICH1: encoding protein QRICH1, also known as Glutamine-rich protein 1,

RBM6: RNA-binding protein 6

RPP14: Ribonuclease P protein subunit p14

SCN5A: sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)

SETD5: SET domain containing 5

SFMBT1: Scm-like with four mbt domains 1

SLC25A20: solute carrier family 25 (carnitine/acylcarnitine translocase), member 20

STT3B: catalytic subunit of the oligosaccharyltransferase complex

SYNPR: synaptoporin

TAFA4: encoding protein Family with sequence similarity 19 member A4, C-C motif chemokine like

TCAIM: encoding protein T-cell activation inhibitor, mitochondrial

TDGF1: Teratocarcinoma-derived growth factor 1

TMEM158: Transmembrane protein 158

TMIE: transmembrane inner ear

TRAK1: trafficking kinesin-binding protein 1

TRANK1: encoding protein Tetratricopeptide repeat and ankyrin repeat containing 1

TTLL3: encoding protein Tubulin tyrosine ligase-like family, member 3

TUSC2: tumor suppressor candidate 2

UCN2: Urocortin-2

ULK4: UNC-51 like kinase 4

VGLL3: vestigial-like family member 3

VHL: von Hippel-Lindau tumor suppressor

ZMYND10: zinc finger MYND-type containing 10

ZNF197: encoding protein Zinc finger protein 197

ZNF502: encoding protein Zinc finger protein 502

ZNF620: encoding protein Zinc finger protein 620

ZNF621: encoding protein Zinc finger protein 621

ZNF717: encoding protein Zinc finger protein 717


Partial list of the genes located on q-arm (long arm) of human chromosome 3:

ADIPOQ: adiponectin

AMOTL2: encoding protein Angiomotin-like protein 2

ARHGAP31: Rho GRPase activating protein 31


C3orf70 chromosome 3 open reading frame 70

CAMPD1: Camptodactyly

CCDC80: Coiled-coil domain containing protein 80

CD200R1: Cell surface glycoprotein CD200 receptor 1

CHST13: encoding protein Carbohydrate (chondroitin 4) sulfotransferase 13

CLDND1: Claudin domain containing 1

CPN2: Carboxypeptidase N subunit 2

CPOX: coproporphyrinogen oxidase (coproporphyria, harderoporphyria)

DPPA2: Developmental pluripotency associated 2

DTX3L: encoding protein Deltex e3 ubiquitin ligase 3l

DZIP3: encoding protein DAZ interacting zinc finger protein 3

EAF2: ELL associated factor 2

EFCC1: EF-hand and coiled-coil domain containing 1

ETM1: Essential tremor 1

ETV5: ETS variant 5

FAM3D: family with sequence similarity 3, member D

FAM43A: family with sequence similarity 43 member A

FAM162A: family with sequence similarity 162 member A

FBXO40: encoding protein F-box protein 40

FILIP1L: encoding protein Filamin A interacting protein 1 like

GYG1: Glycogenin-1

HACD2 encoding protein 3-hydroxyacyl-CoA dehydratase 2

HGD: homogentisate 1,2-dioxygenase (homogentisate oxidase)

IFT122: intraflagellar transport gene 122

KIAA1257: KIAA1257

LINC01279: encoding protein long intergenic non-protein coding RNA 1279

LNCR5: encoding protein lung cancer susceptibility 5

LMLN: encoding protein Leishmanolysin-like (metallopeptidase M8 family)

LRRC15: leucine rich repeat containing 15

LSG1: large subunit GTPase 1 homolog

MB21D2: encoding protein Mab-21 domain containing 2

MCCC1: methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)

MORC1: encoding protein Morc family cw-type zinc finger 1

MYLK: Telokin

NEPRO: encoding protein Nucleolus and neural progenitor protein

NFKBIZ: NF-kappa-B inhibitor zeta

OTOL1: encoding glycoprotein Otolin

PARP14 encoding protein Poly(ADP-ribose) polymerase family member 14

PCCB: propionyl Coenzyme A carboxylase, beta polypeptide

PDCD10: programmed cell death 10

PIK3CA: phosphoinositide-3-kinase, catalytic, alpha polypeptide

PISRT1: long non-coding RNA

PROSER1: Proline and serine rich protein 1

RAB7: RAB7, member RAS oncogene family

RASA2: encoding protein Ras p21 protein activator 2

RETNLB: resistin-like beta

RHO: rhodopsin visual pigment

RIOX2: Ribosomal oxygenase 2

SELT: Selenoprotein T

SENP7: Sentrin-specific protease 7

SERP1: Stress-associated endoplasmic reticulum protein 1

SOX2: transcription factor

SOX2OT: SOX2 overlapping transcript

SPG14 encoding protein Spastic paraplegia 14 (autosomal recessive)

SRPRB: Signal recognition particle receptor subunit beta

TEX55: encoding protein Testis expressed 55

TMEM44: encoding protein Transmembrane protein 44

TM4SF1: Transmembrane 4 L6 family member 1

TMPRSS7: encoding protein Transmembrane serine protease 7

TP63: Tumor protein p63

TRAT1: T-cell receptor-associated transmembrane adapter 1

USH3A: Usher syndrome 3A

ZBED2: encoding protein Zinc finger BED-type containing 2

ZNF9: zinc finger protein 9 (a cellular retroviral nucleic acid binding protein)


The following diseases and disorders are some of those related to genes on chromosome

3-Methylcrotonyl-CoA carboxylase deficiency

3q29 microdeletion syndrome

Acute myeloid leukemia (AML)


Arrhythmogenic right ventricular dysplasia



Autosomal dominant optic atrophy

ADOA plus syndrome

Biotinidase deficiency

Blepharophimosis, epicanthus inversus and ptosis type 1

Breast/colon/lung/pancreatic cancer

Brugada syndrome

Castillo fever

Carnitine-acylcarnitine translocase deficiency


Cerebral cavernous malformation

Charcot–Marie–Tooth disease, type 2

Charcot–Marie–Tooth disease

Chromosome 3q duplication syndrome


A location on human chromosome 3 is associated with respiratory failure and possibly with increased severity in COVID-19

Dandy–Walker syndrome



Dystrophic epidermolysis bullosa

Endplate acetylcholinesterase deficiency

Essential tremors

Ectrodactyly, Case 4

Glaucoma, primary open angle

Glycogen storage disease

Hailey–Hailey disease


Heart block, progressive/nonprogressive

Hereditary coproporphyria

Hereditary nonpolyposis colorectal cancer

HIV infection, susceptibility/resistance to

Hypobetalipoproteinemia, familial


Leukoencephalopathy with vanishing white matter

Long QT syndrome


Malignant hyperthermia susceptibility

Metaphyseal chondrodysplasia, Murk Jansen type


Möbius syndrome

Moyamoya disease


Muir–Torre family cancer syndrome

Myotonic dystrophy

Neuropathy, hereditary motor and sensory, Okinawa type

Night blindness

Nonsyndromic deafness

Ovarian cancer


Propionic acidemia

Protein S deficiency

Pseudo-Zellweger syndrome

Retinitis pigmentosa

Romano–Ward syndrome

Seckel syndrome

Sensenbrenner syndrome

Septo-optic dysplasia

Short stature

Spinocerebellar ataxia

Sucrose intolerance

T-cell leukemia translocation altered gene

Usher syndrome

von Hippel–Lindau syndrome

Waardenburg syndrome

Xeroderma pigmentosum, complementation group c

Cytogenetic band

G-banding ideograms of human chromosome 3

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