Human Phenotype Ontology 
Grandparent Node:
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Abnormality of skin morphology (HP:0011121)help
Parent Node:
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Abnormality of skin pigmentation (HP:0001000)help
..Starting node
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Freckling (HP:0001480)help
Term ID: 1480
Name: Freckling
Synonym: Freckling
Definition: The presence of an increased number of freckles, small circular spots on the skin that are darker than the surrounding skin because of deposits of melanin.
Comments:
Reference: HP:0001480
Genes and Diseases:
 
       Child Nodes:
........expandAxillary freckling (HP:0000997) help
........expandInguinal freckling (HP:0030052) help

 Sister Nodes: 
..expandAbnormality of dermal melanosomes (HP:0011125) help
..expandBlotching pigmentation of the skin (HP:0007610) help
..expandDepigmentation/hyperpigmentation of skin (HP:0007483) help
..expandFine, reticulate skin pigmentation (HP:0007617) help
..expandHyperpigmentation of the skin (HP:0000953) help
..expandHypopigmentation of the skin (HP:0001010) help
..expandMelanocytic nevus (HP:0000995) help
..expandMottled pigmentation (HP:0001070) help
..expandNumerous pigmented freckles (HP:0007587) help
..expandPerioral hyperpigmentation (HP:0010802) help
..expandPeriorbital hyperpigmentation (HP:0001106) help
..expandPigmentation anomalies of sun-exposed skin (HP:0007623) help
..expandProfuse pigmented skin lesions (HP:0005587) help
..expandReticulated skin pigmentation (HP:0007427) help
..expandSymmetric great toe depigmentation (HP:0200015) help
..expandVitiligo (HP:0001045) help
InputHPO IDHPO termDistanceGeneGene id entrezHGNC IDDiseaseIdDiseaseNameFrequencyOnsetHGMD variantsClinVar variants
 
HPO disease - gene - phenotype typical associations:
 
HPO disease - gene - phenotype less frequent non-typical associations:
HP:0001480HP:0001480Freckling0ABCB6 CL E G H1005847ORPHA:241Dyschromatosis universalis hereditariaHP:0040282 - Frequent20
HP:0001480HP:0001480Freckling0ACD CL E G H6505725070ORPHA:618Familial melanomaHP:0040282 - Frequent11
HP:0001480HP:0001480Freckling0AP3D1 CL E G H8943568ORPHA:54X-linked recessive ocular albinismHP:0040282 - Frequent1
HP:0001480HP:0001480Freckling0BAP1 CL E G H8314950ORPHA:618Familial melanomaHP:0040282 - Frequent184
HP:0001480HP:0001480Freckling0BRAF CL E G H6731097ORPHA:500Noonan syndrome with multiple lentiginesHP:0040281 - Very frequent276
HP:0001480HP:0001480Freckling0CDH3 CL E G H10011762ORPHA:1573Hypotrichosis with juvenile macular degenerationHP:0040283 - Occasional87
HP:0001480HP:0001480Freckling0CDK4 CL E G H10191773ORPHA:618Familial melanomaHP:0040282 - Frequent145
HP:0001480HP:0001480Freckling0CDKN2A CL E G H10291787ORPHA:618Familial melanomaHP:0040282 - Frequent289
HP:0001480HP:0001480Freckling0CDKN2B CL E G H10301788ORPHA:618Familial melanomaHP:0040282 - Frequent1
HP:0001480HP:0001480Freckling0DDB2 CL E G H16432718ORPHA:910Xeroderma pigmentosumHP:0040281 - Very frequent30
HP:0001480HP:0001480Freckling0ERCC2 CL E G H20683434OMIM:601675Trichothiodystrophy 1, photosensitive.106
HP:0001480HP:0001480Freckling0ERCC2 CL E G H20683434ORPHA:910Xeroderma pigmentosumHP:0040281 - Very frequent106
HP:0001480HP:0001480Freckling0ERCC3 CL E G H20713435ORPHA:910Xeroderma pigmentosumHP:0040281 - Very frequent54
HP:0001480HP:0001480Freckling0ERCC3 CL E G H20713435OMIM:610651Xeroderma pigmentosum, complementation group B.54
HP:0001480HP:0001480Freckling0ERCC4 CL E G H20723436ORPHA:910Xeroderma pigmentosumHP:0040281 - Very frequent158
HP:0001480HP:0001480Freckling0ERCC4 CL E G H20723436OMIM:278760Xeroderma pigmentosum, complementation group F158
HP:0001480HP:0001480Freckling0ERCC5 CL E G H20733437ORPHA:910Xeroderma pigmentosumHP:0040281 - Very frequent83
HP:0001480HP:0001480Freckling0ERCC6 CL E G H20743438OMIM:600630Uv-Sensitive syndrome 1.199
HP:0001480HP:0001480Freckling0ERCC8 CL E G H11613439OMIM:614621UV-sensitive syndrome 2.55
HP:0001480HP:0001480Freckling0GPR143 CL E G H493520145ORPHA:54X-linked recessive ocular albinismHP:0040282 - Frequent64
HP:0001480HP:0001480Freckling0HPS1 CL E G H32575163OMIM:203300Hermansky-Pudlak syndrome 1.121
HP:0001480HP:0001480Freckling0KAT6A CL E G H799413013OMIM:616268Arboleda-Tham syndrome34
HP:0001480HP:0001480Freckling0KRT5 CL E G H38526442ORPHA:79145Dowling-Degos disease173
HP:0001480HP:0001480Freckling0MC1R CL E G H41576929ORPHA:618Familial melanomaHP:0040282 - Frequent124
HP:0001480HP:0001480Freckling0MC1R CL E G H41576929ORPHA:79432Oculocutaneous albinism type 2HP:0040282 - Frequent124
HP:0001480HP:0001480Freckling0MGMT CL E G H42557059ORPHA:618Familial melanomaHP:0040282 - Frequent3
HP:0001480HP:0001480Freckling0MITF CL E G H42867105ORPHA:618Familial melanomaHP:0040282 - Frequent91
HP:0001480HP:0001480Freckling0MLH1 CL E G H42927127OMIM:276300Mismatch repair cancer syndrome 11819
HP:0001480HP:0001480Freckling0MSH6 CL E G H29567329OMIM:619097MISMATCH REPAIR CANCER SYNDROME 3; MMRCS32232
HP:0001480HP:0001480Freckling0NBN CL E G H46837652ORPHA:647Nijmegen breakage syndromeHP:0040283 - Occasional706
HP:0001480HP:0001480Freckling0NF1 CL E G H47637765ORPHA:9768517q11 microdeletion syndromeHP:0040281 - Very frequent1952
HP:0001480HP:0001480Freckling0NF1 CL E G H47637765ORPHA:363700Neurofibromatosis type 1 due to NF1 mutation or intragenic deletion1952
HP:0001480HP:0001480Freckling0NF1 CL E G H47637765OMIM:162200Neurofibromatosis, type I1952
HP:0001480HP:0001480Freckling0NF1 CL E G H47637765OMIM:601321Neurofibromatosis-Noonan syndrome1952
HP:0001480HP:0001480Freckling0NF1 CL E G H47637765OMIM:193520Watson syndrome1952
HP:0001480HP:0001480Freckling0OCA2 CL E G H49488101ORPHA:79432Oculocutaneous albinism type 2HP:0040282 - Frequent121
HP:0001480HP:0001480Freckling0POFUT1 CL E G H2350914988ORPHA:79145Dowling-Degos disease2
HP:0001480HP:0001480Freckling0POGLUT1 CL E G H5698322954ORPHA:79145Dowling-Degos disease6
HP:0001480HP:0001480Freckling0POT1 CL E G H2591317284ORPHA:618Familial melanomaHP:0040282 - Frequent23
HP:0001480HP:0001480Freckling0PPP1CB CL E G H55009282OMIM:617506Noonan syndrome-like disorder with loose anagen hair 29
HP:0001480HP:0001480Freckling0PRKAR1A CL E G H55739388OMIM:160980Carney complex, type 1.134
HP:0001480HP:0001480Freckling0PSENEN CL E G H5585130100ORPHA:79145Dowling-Degos disease2
HP:0001480HP:0001480Freckling0PTPN11 CL E G H57819644ORPHA:500Noonan syndrome with multiple lentiginesHP:0040281 - Very frequent291
HP:0001480HP:0001480Freckling0RAF1 CL E G H58949829ORPHA:500Noonan syndrome with multiple lentiginesHP:0040281 - Very frequent212
HP:0001480HP:0001480Freckling0SOX18 CL E G H5434511194OMIM:137940Hypotrichosis-Lymphedema-Telangiectasia-Renal defect syndrome.7
HP:0001480HP:0001480Freckling0SPRED1 CL E G H16174220249ORPHA:137605Legius syndrome136
HP:0001480HP:0001480Freckling0SPRED1 CL E G H16174220249OMIM:611431Legius syndrome136
HP:0001480HP:0001480Freckling0TERF2IP CL E G H5438619246ORPHA:618Familial melanomaHP:0040282 - Frequent
HP:0001480HP:0001480Freckling0TERT CL E G H701511730ORPHA:618Familial melanomaHP:0040282 - Frequent238
HP:0001480HP:0001480Freckling0TP63 CL E G H862615979ORPHA:978ADULT syndromeHP:0040281 - Very frequent140
HP:0001480HP:0001480Freckling0TP63 CL E G H862615979OMIM:103285Adult syndrome.140
HP:0001480HP:0001480Freckling0TP63 CL E G H862615979ORPHA:69085Limb-mammary syndromeHP:0040284 - Very rare140
HP:0001480HP:0001480Freckling0TYR CL E G H729912442ORPHA:79431Oculocutaneous albinism type 1AHP:0040282 - Frequent146
HP:0001480HP:0001480Freckling0TYR CL E G H729912442ORPHA:79434Oculocutaneous albinism type 1BHP:0040281 - Very frequent146
HP:0001480HP:0001480Freckling0TYRP1 CL E G H730612450ORPHA:79433Oculocutaneous albinism type 3HP:0040282 - Frequent62
HP:0001480HP:0001480Freckling0UVSSA CL E G H5765429304OMIM:614640Uv-Sensitive syndrome 3.3
HP:0001480HP:0001480Freckling0XPA CL E G H750712814ORPHA:910Xeroderma pigmentosumHP:0040281 - Very frequent34
HP:0001480HP:0001480Freckling0XPC CL E G H750812816ORPHA:910Xeroderma pigmentosumHP:0040281 - Very frequent86
HP:0001480HP:0030052Inguinal freckling1KRT5 CL E G H38526442ORPHA:79145Dowling-Degos diseaseHP:0040282 - Frequent173
HP:0001480HP:0000997Axillary freckling1MLH1 CL E G H42927127OMIM:276300Mismatch repair cancer syndrome 11819
HP:0001480HP:0000997Axillary freckling1MSH6 CL E G H29567329OMIM:619097MISMATCH REPAIR CANCER SYNDROME 3; MMRCS32232
HP:0001480HP:0000997Axillary freckling1NF1 CL E G H47637765ORPHA:363700Neurofibromatosis type 1 due to NF1 mutation or intragenic deletionHP:0040282 - Frequent1952
HP:0001480HP:0030052Inguinal freckling1NF1 CL E G H47637765ORPHA:363700Neurofibromatosis type 1 due to NF1 mutation or intragenic deletionHP:0040282 - Frequent1952
HP:0001480HP:0000997Axillary freckling1NF1 CL E G H47637765OMIM:162200Neurofibromatosis, type I1952
HP:0001480HP:0030052Inguinal freckling1NF1 CL E G H47637765OMIM:162200Neurofibromatosis, type I1952
HP:0001480HP:0000997Axillary freckling1NF1 CL E G H47637765OMIM:601321Neurofibromatosis-Noonan syndrome1952
HP:0001480HP:0030052Inguinal freckling1NF1 CL E G H47637765OMIM:601321Neurofibromatosis-Noonan syndrome1952
HP:0001480HP:0000997Axillary freckling1NF1 CL E G H47637765OMIM:193520Watson syndrome.1952
HP:0001480HP:0030052Inguinal freckling1NF1 CL E G H47637765OMIM:193520Watson syndrome1952
HP:0001480HP:0030052Inguinal freckling1POFUT1 CL E G H2350914988ORPHA:79145Dowling-Degos diseaseHP:0040282 - Frequent2
HP:0001480HP:0030052Inguinal freckling1POGLUT1 CL E G H5698322954ORPHA:79145Dowling-Degos diseaseHP:0040282 - Frequent6
HP:0001480HP:0030052Inguinal freckling1PSENEN CL E G H5585130100ORPHA:79145Dowling-Degos diseaseHP:0040282 - Frequent2
HP:0001480HP:0000997Axillary freckling1SPRED1 CL E G H16174220249ORPHA:137605Legius syndrome136
HP:0001480HP:0030052Inguinal freckling1SPRED1 CL E G H16174220249ORPHA:137605Legius syndrome136
HP:0001480HP:0000997Axillary freckling1SPRED1 CL E G H16174220249OMIM:611431Legius syndrome.136


Genes (46) :ABCB6 ACD AP3D1 BAP1 BRAF CDH3 CDK4 CDKN2A CDKN2B DDB2 ERCC2 ERCC3 ERCC4 ERCC5 ERCC6 ERCC8 GPR143 HPS1 KAT6A KRT5 MC1R MGMT MITF MLH1 MSH6 NBN NF1 OCA2 POFUT1 POGLUT1 POT1 PPP1CB PRKAR1A PSENEN PTPN11 RAF1 SOX18 SPRED1 TERF2IP TERT TP63 TYR TYRP1 UVSSA XPA XPC

Diseases (35) :ORPHA:241 ORPHA:618 ORPHA:54 ORPHA:500 ORPHA:1573 ORPHA:910 OMIM:601675 OMIM:610651 OMIM:278760 OMIM:600630 OMIM:614621 OMIM:203300 OMIM:616268 ORPHA:79145 ORPHA:79432 OMIM:276300 OMIM:619097 ORPHA:647 ORPHA:97685 ORPHA:363700 OMIM:162200 OMIM:601321 OMIM:193520 OMIM:617506 OMIM:160980 OMIM:137940 ORPHA:137605 OMIM:611431 ORPHA:978 OMIM:103285 ORPHA:69085 ORPHA:79431 ORPHA:79434 ORPHA:79433 OMIM:614640
 

Human Phenotype Ontology(HPO) is developed by the Human Phenotype Ontology Consortium. The version used here is December 15 2022 release.