GEPHE SUMMARY
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Gephebase Gene
Entry Status
Published
GepheID
GP00001363
Main curator
Prigent
PHENOTYPIC CHANGE
Trait Category
Trait State in Taxon A
DNA repair in darker skin tones in various populations
Trait State in Taxon B
DNA repair associated with lighter skin tones in Eurasia
Ancestral State
Taxon A
Taxonomic Status
Taxon A
Latin Name
Common Name
human
Synonyms
human; man; Homo sapiens Linnaeus, 1758; Home sapiens; Homo sampiens; Homo sapeins; Homo sapian; Homo sapians; Homo sapien; Homo sapience; Homo sapiense; Homo sapients; Homo sapines; Homo spaiens; Homo spiens; Humo sapiens
Rank
species
Lineage
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opterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo
Parent
NCBI Taxonomy ID
is Taxon A an Infraspecies?
No
Taxon B
Latin Name
Common Name
human
Synonyms
human; man; Homo sapiens Linnaeus, 1758; Home sapiens; Homo sampiens; Homo sapeins; Homo sapian; Homo sapians; Homo sapien; Homo sapience; Homo sapiense; Homo sapients; Homo sapines; Homo spaiens; Homo spiens; Humo sapiens
Rank
species
Lineage
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opterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo
Parent
NCBI Taxonomy ID
is Taxon B an Infraspecies?
No
GENOTYPIC CHANGE
Generic Gene Name
DDB1
Synonyms
XPE; DDBA; XAP1; XPCE; XPE-BF; UV-DDB1
String
Sequence Similarities
Belongs to the DDB1 family.
GO - Molecular Function
GO:0003677 : DNA binding
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GO - Biological Process
GO:0016567 : protein ubiquitination
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GO - Cellular Component
GO:0005737 : cytoplasm
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UniProtKB
Homo sapiens
Homo sapiens
Presumptive Null
Molecular Type
Aberration Type
Molecular Details of the Mutation
most strongly associated SNPs are located in a region conserved across vertebrates flanked by TMEM138 and TMEM216 ~36 to 44 kb upstream of DDB1 and in high LD ; includes rs7948623 located 172 bp downstream of TMEM138 which shows enhancer activity in melanoma cells and interacts with the promoters of DDB1
Experimental Evidence
Authors
Crawford NG; Kelly DE; Hansen MEB; Beltrame MH; Fan S; Bowman SL; Jewett E; Ranciaro A; et al.
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Abstract
Despite the wide range of skin pigmentation in humans, little is known about its genetic basis in global populations. Examining ethnically diverse African genomes, we identify variants in or near SLC24A5, MFSD12, DDB1, TMEM138, OCA2, and HERC2 that are significantly associated with skin pigmentation. Genetic evidence indicates that the light pigmentation variant at SLC24A5 was introduced into East Africa by gene flow from non-Africans. At all other loci, variants associated with dark pigmentation in Africans are identical by descent in South Asian and Australo-Melanesian populations. Functional analyses indicate that MFSD12 encodes a lysosomal protein that affects melanogenesis in zebrafish and mice, and that mutations in melanocyte-specific regulatory regions near DDB1/TMEM138 correlate with expression of ultraviolet response genes under selection in Eurasians.
Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.
Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.
Additional References
RELATED GEPHE
Related Genes
No matches found.
Related Haplotypes
No matches found.
EXTERNAL LINKS
COMMENTS
possible selective sweep with high levels of homozygosity extending ~350 to 550 kb in Europeans and Asians
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