LOCUS       NM_205850               1879 bp    mRNA    linear   PRI 04-OCT-2024
DEFINITION  Homo sapiens solute carrier family 24 member 5 (SLC24A5), mRNA.
ACCESSION   NM_205850 XM_208771
VERSION     NM_205850.3
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 1879)
  AUTHORS   Ang,K.C., Canfield,V.A., Foster,T.C., Harbaugh,T.D., Early,K.A.,
            Harter,R.L., Reid,K.P., Leong,S.L., Kawasawa,Y., Liu,D.,
            Hawley,J.W. and Cheng,K.C.
  TITLE     Native American genetic ancestry and pigmentation allele
            contributions to skin color in a Caribbean population
  JOURNAL   Elife 12, e77514 (2023)
   PUBMED   37294081
  REMARK    GeneRIF: Native American genetic ancestry and pigmentation allele
            contributions to skin color in a Caribbean population.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1879)
  AUTHORS   Yousaf,S., Sethna,S., Chaudhary,M.A., Shaikh,R.S., Riazuddin,S. and
            Ahmed,Z.M.
  TITLE     Molecular characterization of SLC24A5 variants and evaluation of
            Nitisinone treatment efficacy in a zebrafish model of OCA6
  JOURNAL   Pigment Cell Melanoma Res 33 (4), 556-565 (2020)
   PUBMED   32274888
  REMARK    GeneRIF: Molecular characterization of SLC24A5 variants and
            evaluation of Nitisinone treatment efficacy in a zebrafish model of
            OCA6.
REFERENCE   3  (bases 1 to 1879)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   4  (bases 1 to 1879)
  AUTHORS   Zhang,Y., Zhang,Y., Liu,T., Bai,D., Yang,X., Li,W. and Wei,A.
  TITLE     Identification of two Chinese oculocutaneous albinism type 6
            patients and mutation updates of the SLC24A5 gene
  JOURNAL   J Dermatol 46 (11), 1027-1030 (2019)
   PUBMED   31486119
  REMARK    GeneRIF: This study identifies two novel SLC24A5 frame-shift
            variants in two unrelated Chinese oculocutaneous albinism type 6
            patients.
REFERENCE   5  (bases 1 to 1879)
  AUTHORS   Lin,M., Siford,R.L., Martin,A.R., Nakagome,S., Moller,M.,
            Hoal,E.G., Bustamante,C.D., Gignoux,C.R. and Henn,B.M.
  TITLE     Rapid evolution of a skin-lightening allele in southern African
            KhoeSan
  JOURNAL   Proc Natl Acad Sci U S A 115 (52), 13324-13329 (2018)
   PUBMED   30530665
  REMARK    GeneRIF: The derived causal allele in SLC24A5, p.Ala111Thr,
            significantly lightens basal skin pigmentation in the KhoeSan and
            explains 8 to 15% of phenotypic variance in these populations. The
            frequency of this allele (33 to 53%) is far greater than expected
            from gene flow.  We show that the allele was introduced into the
            KhoeSan only 2,000 y ago via a back-to-Africa migration and then
            experienced a selective sweep.
REFERENCE   6  (bases 1 to 1879)
  AUTHORS   Sulem,P., Gudbjartsson,D.F., Stacey,S.N., Helgason,A., Rafnar,T.,
            Magnusson,K.P., Manolescu,A., Karason,A., Palsson,A.,
            Thorleifsson,G., Jakobsdottir,M., Steinberg,S., Palsson,S.,
            Jonasson,F., Sigurgeirsson,B., Thorisdottir,K., Ragnarsson,R.,
            Benediktsdottir,K.R., Aben,K.K., Kiemeney,L.A., Olafsson,J.H.,
            Gulcher,J., Kong,A., Thorsteinsdottir,U. and Stefansson,K.
  TITLE     Genetic determinants of hair, eye and skin pigmentation in
            Europeans
  JOURNAL   Nat Genet 39 (12), 1443-1452 (2007)
   PUBMED   17952075
REFERENCE   7  (bases 1 to 1879)
  AUTHORS   Soejima,M. and Koda,Y.
  TITLE     Population differences of two coding SNPs in pigmentation-related
            genes SLC24A5 and SLC45A2
  JOURNAL   Int J Legal Med 121 (1), 36-39 (2007)
   PUBMED   16847698
  REMARK    GeneRIF: The p.L374F allele in SLC45A2 is a more specific ancestry
            informative marker than the p.A111T allele in SLC24A5, as it
            clearly distinguishes Sri Lankans from Europeans.
REFERENCE   8  (bases 1 to 1879)
  AUTHORS   Chi,A., Valencia,J.C., Hu,Z.Z., Watabe,H., Yamaguchi,H.,
            Mangini,N.J., Huang,H., Canfield,V.A., Cheng,K.C., Yang,F., Abe,R.,
            Yamagishi,S., Shabanowitz,J., Hearing,V.J., Wu,C., Appella,E. and
            Hunt,D.F.
  TITLE     Proteomic and bioinformatic characterization of the biogenesis and
            function of melanosomes
  JOURNAL   J Proteome Res 5 (11), 3135-3144 (2006)
   PUBMED   17081065
REFERENCE   9  (bases 1 to 1879)
  AUTHORS   Lamason,R.L., Mohideen,M.A., Mest,J.R., Wong,A.C., Norton,H.L.,
            Aros,M.C., Jurynec,M.J., Mao,X., Humphreville,V.R., Humbert,J.E.,
            Sinha,S., Moore,J.L., Jagadeeswaran,P., Zhao,W., Ning,G.,
            Makalowska,I., McKeigue,P.M., O'donnell,D., Kittles,R., Parra,E.J.,
            Mangini,N.J., Grunwald,D.J., Shriver,M.D., Canfield,V.A. and
            Cheng,K.C.
  TITLE     SLC24A5, a putative cation exchanger, affects pigmentation in
            zebrafish and humans
  JOURNAL   Science 310 (5755), 1782-1786 (2005)
   PUBMED   16357253
  REMARK    GeneRIF: the variant allele is associated with a substantial
            reduction in regional heterozygosity, and correlates with lighter
            skin pigmentation in admixed populations, suggesting a key role for
            the SLC24A5 gene in human pigmentation
REFERENCE   10 (bases 1 to 1879)
  AUTHORS   Thomas,M.G., Zippin,J. and Brooks,B.P.
  TITLE     Oculocutaneous Albinism and Ocular Albinism Overview
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   37053367
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AF348468.1, BC073944.1 and
            AC090526.3.
            This sequence is a reference standard in the RefSeqGene project.
            
            On May 17, 2019 this sequence version replaced NM_205850.2.
            
            Summary: This gene is a member of the potassium-dependent
            sodium/calcium exchanger family and encodes an intracellular
            membrane protein with 2 large hydrophilic loops and 2 sets of
            multiple transmembrane-spanning segments. Sequence variation in
            this gene has been associated with differences in skin
            pigmentation. [provided by RefSeq, Jul 2008].
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC143950.1, DQ665306.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2145893, SAMEA2147596
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000341459.8/ ENSP00000341550.3
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1128              AF348468.1         19-1146
            1129-1558           BC073944.1         228-657
            1559-1599           AF348468.1         1577-1617
            1600-1879           AC090526.3         154817-155096
FEATURES             Location/Qualifiers
     source          1..1879
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="15"
                     /map="15q21.1"
     gene            1..1879
                     /gene="SLC24A5"
                     /gene_synonym="JSX; NCKX5; OCA6; SHEP4"
                     /note="solute carrier family 24 member 5"
                     /db_xref="GeneID:283652"
                     /db_xref="HGNC:HGNC:20611"
                     /db_xref="MIM:609802"
     exon            1..176
                     /gene="SLC24A5"
                     /gene_synonym="JSX; NCKX5; OCA6; SHEP4"
                     /inference="alignment:Splign:2.1.0"
     CDS             56..1558
                     /gene="SLC24A5"
                     /gene_synonym="JSX; NCKX5; OCA6; SHEP4"
                     /note="ion transporter JSX; sodium/potassium/calcium
                     exchanger 5; Na/Ca-K exchanger 5;
                     Na(+)/K(+)/Ca(2+)-exchange protein 5; solute carrier
                     family 24 (sodium/potassium/calcium exchanger), member 5;
                     oculocutaneous albinism 6 (autosomal recessive)"
                     /codon_start=1
                     /product="sodium/potassium/calcium exchanger 5 precursor"
                     /protein_id="NP_995322.1"
                     /db_xref="CCDS:CCDS10128.1"
                     /db_xref="GeneID:283652"
                     /db_xref="HGNC:HGNC:20611"
                     /db_xref="MIM:609802"
                     /translation="MQTKGGQTWARRALLLGILWATAHLPLSGTSLPQRLPRATGNST
                     QCVISPSSEFPEGFFTRQERRDGGIIIYFLIIVYMFMAISIVCDEYFLPSLEIISESL
                     GLSQDVAGTTFMAAGSSAPELVTAFLGVFITKGDIGISTILGSAIYNLLGICAACGLL
                     SNTVSTLSCWPLFRDCAAYTISAAAVLGIIYDNQVYWYEGALLLLIYGLYVLVLCFDI
                     KINQYIIKKCSPCCACLAKAMERSEQQPLMGWEDEGQPFIRRQSRTDSGIFYEDSGYS
                     QLSISLHGLSQVSEDPPSVFNMPEADLKRIFWVLSLPIITLLFLTTPDCRKKFWKNYF
                     VITFFMSAIWISAFTYILVWMVTITGETLEIPDTVMGLTLLAAGTSIPDTIASVLVAR
                     KGKGDMAMSNIVGSNVFDMLCLGIPWFIKTAFINGSAPAEVNSRGLTYITISLNISII
                     FLFLAVHFNGWKLDRKLGIVCLLSYLGLATLSVLYELGIIGNNKIRGCGG"
     exon            177..356
                     /gene="SLC24A5"
                     /gene_synonym="JSX; NCKX5; OCA6; SHEP4"
                     /inference="alignment:Splign:2.1.0"
     exon            357..440
                     /gene="SLC24A5"
                     /gene_synonym="JSX; NCKX5; OCA6; SHEP4"
                     /inference="alignment:Splign:2.1.0"
     exon            441..544
                     /gene="SLC24A5"
                     /gene_synonym="JSX; NCKX5; OCA6; SHEP4"
                     /inference="alignment:Splign:2.1.0"
     exon            545..645
                     /gene="SLC24A5"
                     /gene_synonym="JSX; NCKX5; OCA6; SHEP4"
                     /inference="alignment:Splign:2.1.0"
     exon            646..926
                     /gene="SLC24A5"
                     /gene_synonym="JSX; NCKX5; OCA6; SHEP4"
                     /inference="alignment:Splign:2.1.0"
     exon            927..1133
                     /gene="SLC24A5"
                     /gene_synonym="JSX; NCKX5; OCA6; SHEP4"
                     /inference="alignment:Splign:2.1.0"
     exon            1134..1235
                     /gene="SLC24A5"
                     /gene_synonym="JSX; NCKX5; OCA6; SHEP4"
                     /inference="alignment:Splign:2.1.0"
     exon            1236..1879
                     /gene="SLC24A5"
                     /gene_synonym="JSX; NCKX5; OCA6; SHEP4"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1537..1542
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SLC24A5"
                     /gene_synonym="JSX; NCKX5; OCA6; SHEP4"
                     /note="hexamer: AATAAG"
     polyA_site      1563
                     /gene="SLC24A5"
                     /gene_synonym="JSX; NCKX5; OCA6; SHEP4"
                     /note="major polyA site"
ORIGIN      
        1 aatcctcctc ttctcccttc ctgaagctgc acgctgcagt aagagcacag cagaaatgca
       61 gacaaaaggg ggccaaacat gggcgagaag ggctctgttg ctcggcatcc tgtgggccac
      121 tgcacatctg cctctctcag ggacctccct gccccaacgt ctcccaaggg ccacaggaaa
      181 tagcacccaa tgtgttattt ctccatcatc ggagtttccc gaagggtttt tcacgagaca
      241 ggagcgcaga gatggaggca tcataatcta tttcctaatt atcgtttaca tgttcatggc
      301 catatctatt gtctgtgatg aatacttcct accctccctg gaaatcatca gtgaatccct
      361 tggattgtct caggatgttg caggcacaac tttcatggca gcgggcagtt cagctcctga
      421 attagttact gctttcctag gtgtatttat cacaaaggga gatattggca ttagcaccat
      481 ccttggatct gcaatttata atctccttgg catctgtgct gcctgtggtt tgctatctaa
      541 tacggtctca acactatcat gttggcccct attcagagac tgtgcagcgt acacaattag
      601 tgcagcagca gttcttggta taatatatga caaccaagtt tactggtatg aaggggcttt
      661 actgcttttg atatatggat tgtatgtttt ggtgctgtgt tttgacatta aaattaacca
      721 atatattata aagaaatgca gtccttgctg cgcctgtctt gccaaagcta tggagagaag
      781 tgaacaacag ccactgatgg gctgggaaga tgaaggtcaa ccattcattc gtcggcaatc
      841 aagaactgat agtggaatat tttatgaaga ttctggctac tctcagctct ctataagttt
      901 acatggcctt agtcaggttt ctgaagatcc accaagtgtt ttcaacatgc ctgaagcaga
      961 cttaaaaaga attttttggg tattatccct tcctattatt acattacttt ttctaaccac
     1021 accagattgt agaaaaaagt tttggaaaaa ctactttgtg ataacctttt tcatgtctgc
     1081 aatatggata tccgcattta catatatcct ggtttggatg gtcacaataa ctggggaaac
     1141 actagaaatt cccgatacag taatgggcct tactttatta gcagcaggaa caagcatacc
     1201 agacacaatt gcaagtgtgt tggttgcaag aaaagggaaa ggagatatgg ctatgtctaa
     1261 catcgtggga tccaatgtgt ttgatatgtt gtgccttggt attccatggt ttattaaaac
     1321 tgcatttata aatggatcag ctcctgcaga agtaaacagc agaggactaa cttacataac
     1381 catctctctc aacatttcaa ttatttttct ttttttagca gttcacttca atggctggaa
     1441 actagacaga aagttgggaa tagtctgcct attatcatac ttggggcttg ctacattatc
     1501 agttctatat gaacttggaa ttattggaaa taataaaata aggggctgtg gaggttgata
     1561 ttattaatag tgttatgcag aaaatatgaa tggcagggag gggcagagag aaaaatccat
     1621 ttcttcattt aaatcaaatt ttaaaaatct tgaaccttag aatctaaaac ttacagtaat
     1681 ttaaaaccaa ccaaaatcac atcctaattt ttctgagccc tttcttttca tgaaaaatta
     1741 catattataa aacagaagtt tggggggaaa aaatctatgt tttaccatac aataagttga
     1801 caaaaactgg agaaactaga acaaacaaat ccaactatgt agtactgaaa acaacaagaa
     1861 aatggcttat ttcattaaa
//
