Gene Gene information from NCBI Gene database.
Entrez ID 7840
Gene name ALMS1 centrosome and basal body associated protein
Gene symbol ALMS1
Synonyms (NCBI Gene)
ALSS
Chromosome 2
Chromosome location 2p13.1
Summary This gene encodes a protein containing a large tandem-repeat domain as well as additional low complexity regions. The encoded protein functions in microtubule organization, particularly in the formation and maintanance of cilia. Mutations in this gene cau
SNPs SNP information provided by dbSNP.
245
SNP ID Visualize variation Clinical significance Consequence
rs35902379 G>T Likely-benign, conflicting-interpretations-of-pathogenicity Coding sequence variant, synonymous variant
rs45596541 C>G,T Likely-benign, conflicting-interpretations-of-pathogenicity Coding sequence variant, missense variant, synonymous variant
rs58806616 A>G Benign, conflicting-interpretations-of-pathogenicity Coding sequence variant, missense variant
rs73945001 A>G Conflicting-interpretations-of-pathogenicity, likely-benign, uncertain-significance Coding sequence variant, missense variant
rs77517267 C>G,T Conflicting-interpretations-of-pathogenicity, benign Coding sequence variant, synonymous variant, missense variant
miRNA miRNA information provided by mirtarbase database.
8
miRTarBase ID miRNA Experiments Reference
MIRT004192 hsa-miR-197-3p Microarray 16822819
MIRT019997 hsa-miR-375 Microarray 20215506
MIRT031049 hsa-miR-21-5p Microarray 18591254
MIRT050457 hsa-miR-22-3p CLASH 23622248
MIRT049216 hsa-miR-92a-3p CLASH 23622248
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
21
GO ID Ontology Definition Evidence Reference
GO:0000922 Component Spindle pole IEA
GO:0005515 Function Protein binding IPI 31413325, 33961781
GO:0005654 Component Nucleoplasm IDA
GO:0005737 Component Cytoplasm IEA
GO:0005739 Component Mitochondrion IDA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
606844 428 ENSG00000116127
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q8TCU4
Protein name Centrosome-associated protein ALMS1 (Alstrom syndrome protein 1)
Protein function Involved in PCM1-dependent intracellular transport. Required, directly or indirectly, for the localization of NCAPD2 to the proximal ends of centrioles. Required for proper formation and/or maintenance of primary cilia (PC), microtubule-based st
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF18727 ALMS_repeat 539 585 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 586 632 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 633 679 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 680 726 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 727 774 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 775 821 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 822 871 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 872 918 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 919 965 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 966 1013 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 1014 1060 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 1061 1107 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 1108 1155 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 1156 1202 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 1203 1249 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 1250 1297 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 1298 1344 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 1345 1392 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 1393 1439 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 1440 1486 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 1487 1534 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 1535 1581 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 1582 1628 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 1629 1675 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 1676 1722 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 1723 1769 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 1770 1816 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 1817 1861 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 1862 1906 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 1907 1951 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 1952 1996 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 1993 2028 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 2059 2105 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 2106 2152 Alstrom syndrome repeat Repeat
PF18727 ALMS_repeat 2153 2199 Alstrom syndrome repeat Repeat
PF15309 ALMS_motif 4032 4164 ALMS motif Family
Tissue specificity TISSUE SPECIFICITY: Expressed in all tissues tested including adipose and pancreas. Expressed by beta-cells of the islets in the pancreas (at protein level). {ECO:0000269|PubMed:11941369, ECO:0000269|PubMed:11941370}.
Sequence
MEPEDLPWPGELEEEEEEEEEEEEEEEEAAAAAAANVDDVVVVEEVEEEAGRELDSDSHY
GPQHLESIDDEEDEEAKAWLQAHPGRILPPLSPPQHRYSEGERTSLEKIVPLTCHVWQQI
VYQGNSRTQISDTNVVCLETTAQRGSGDDQKTESWHCLPQEMDSSQTLDTSQTRFNVRTE
DTEVTDFPSLEEGILTQSENQVKEPNRDLFCSPLLVIQDSFASPDLPLLTCLTQDQEFAP
DSLFHQSELSFAPLRGIPDKSEDTEWSSRPSEVSEALFQATAEVASDLASSRFSVSQHPL
IGSTAVGSQCPFLPSEQGNNEETISSVDELKIPKDCDRYDDLCSYMSWKTRKDTQWPENN
LADKDQVSVATSFDITDENIATKRSDHFDAARSYGQYWTQEDSSKQAETYLTKGLQGKVE
SDVITLDGLNENAVVCSERVAELQRKPTRESEYHSSDLRMLRMSPDTVPKAPKHLKAGDT
SKGGIAKVTQSNLKSGITTTPVDSDIGSHLSLSLEDLSQLAVSSPLETTTGQHTDTLNQK
TLADTHLTEETLKVTAIPEPADQKTATPTVLSSSHSHRGKPSIFY
QQGLPDSHLTEEALK
VSAAPGLADQTTGMSTLTSTSYSHREKPGTFY
QQELPESNLTEEPLEVSAAPGPVEQKTG
IPTVSSTSHSHVEDLLFFY
RQTLPDGHLTDQALKVSAVSGPADQKTGTATVLSTPHSHRE
KPGIFY
QQEFADSHQTEETLTKVSATPGPADQKTEIPAVQSSSYSQREKPSILYPQDLAD
SHLPEEGLKVSAVAGPADQKTGLPTVPSSAYSHREKLLVFY
QQALLDSHLPEEALKVSAV
SGPADGKTGTPAVTSTSSASSSLGEKPSAFY
QQTLPNSHLTEEALKVSIVPGPGDQKTGI
PSAPSSFYSHREKPIIFS
QQTLPDFLFPEEALKVSAVSVLAAQKTGTPTVSSNSHSHSEK
SSVFY
QQELPDSDLPRESLKMSAIPGLTDQKTVPTPTVPSGSFSHREKPSIFYQQEWPDS
YATEKALKVSTGPGPADQKTEIPAVQSSSYPQREKPSVLY
PQVLSDSHLPEESLKVSAFP
GPADQMTDTPAVPSTFYSQREKPGIFY
QQTLPESHLPKEALKISVAPGLADQKTGTPTVT
STSYSQHREKPSIFH
QQALPGTHIPEEAQKVSAVTGPGNQKTWIPRVLSTFYSQREKPGI
FY
QQTLPGSHIPEEAQKVSPVLGPADQKTGTPTPTSASYSHTEKPGIFYQQVLPDNHPTE
EALKISVASEPVDQTTGTPAVTSTSYSQYREKPSIFY
QQSLPSSHLTEEAKNVSAVPGPA
DQKTVIPILPSTFYSHTEKPGVFY
QQVLPHSHPTEEALKISVASEPVDQTTGTPTVTSTS
YSQHTEKPSIFY
QQSLPGSHLTEEAKNVSAVPGPGDRKTGIPTLPSTFYSHTEKPGSFYQ
QVLPHSHLPEEALEVSVAPGPVDQTIGTPTVTSPSSSFGEKPIVIY
KQAFPEGHLPEESL
KVSVAPGPVGQTTGAPTITSPSYSQHRAKSGSFY
QLALLGSQIPEEALRVSSAPGPADQT
TGIPTITSTSYSFGEKPIVNY
KQAFPDGHLPEEALKVSIVSGPTEKKTDIPAGPLGSSAL
GEKPITFY
RQALLDSPLNKEVVKVSAAPGPADQKTETLPVHSTSYSNRGKPVIFYQQTLS
DSHLPEEALKVPPVPGPDAQKTETPSVSSSLYSYREKPIVFY
QQALPDSELTQEALKVSA
VPQPADQKTGLSTVTSSFYSHTEKPNISY
QQELPDSHLTEEALKVSNVPGPADQKTGVST
VTSTSYSHREKPIVSY
QRELPHFTEAGLKILRVPGPADQKTGINILPSNSYPQREHSVIS
Y
EQELPDLTEVTLKAIGVPGPADQKTGIQIASSSSYSNREKASIFHQQELPDVTEEALNV
FVVPGQGDRKTEIPTVPLSYYSRREKPSVIS
QQELPDSHLTEEALKVSPVSIPAEQKTGI
PIGLSSSYSHSH
KEKLKISTVHIPDDQKTEFPAATLSSYSQIEKPKISTVIGPNDQKTPS
QTAFHSSYSQTVKPNILFQQQLPDRDQSKGILKISAVPELTDVNTGKPVSLSSSYFHREK
SNIFS
PQELPGSHVTEDVLKVSTIPGPAGQKTVLPTALPSSFSHREKPDIFYQKDLPDRH
LTEDALKISSALGQADQITGLQTVPSGTYSHGENHKLVS
EHVQRLIDNLNSSDSSVSSNN
VLLNSQADDRVVINKPESAGFRDVGSEEIQDAENSAKTLKEIRTLLMEAENMALKRCNFP
APLARFRDISDISFIQSKKVVCFKEPSSTGVSNGDLLHRQPFTEESPSSRCIQKDIGTQT
NLKCRRGIENWEFISSTTVRSPLQEAESKVSMALEETLRQYQAAKSVMRSEPEGCSGTIG
NKIIIPMMTVIKSDSSSDASDGNGSCSWDSNLPESLESVSDVLLNFFPYVSPKTSITDSR
EEEGVSESEDGGGSSVDSLAAHVKNLLQCESSLNHAKEILRNAEEEESRVRAHAWNMKFN
LAHDCGYSISELNEDDRRKVEEIKAELFGHGRTTDLSKGLQSPRGMGCKPEAVCSHIIIE
SHEKGCFRTLTSEHPQLDRHPCAFRSAGPSEMTRGRQNPSSCRAKHVNLSASLDQNNSHF
KVWNSLQLKSHSPFQNFIPDEFKISKGLRMPFDEKMDPWLSELVEPAFVPPKEVDFHSSS
QMPSPEPMKKFTTSITFSSHRHSKCISNSSVVKVGVTEGSQCTGASVGVFNSHFTEEQNP
PRDLKQKTSSPSSFKMHSNSQDKEVTILAEGRRQSQKLPVDFERSFQEEKPLERSDFTGS
HSEPSTRANCSNFKEIQISDNHTLISMGRPSSTLGVNRSSSRLGVKEKNVTITPDLPSCI
FLEQRELFEQSKAPRADDHVRKHHSPSPQHQDYVAPDLPSCIFLEQRELFEQCKAPYVDH
QMRENHSPLPQGQDSIASDLPSPISLEQCQSKAPGVDDQMNKHHFPLPQGQDCVVEKNNQ
HKPKSHISNINVEAKFNTVVSQSAPNHCTLAASASTPPSNRKALSCVHITLCPKTSSKLD
SGTLDERFHSLDAASKARMNSEFNFDLHTVSSRSLEPTSKLLTSKPVAQDQESLGFLGPK
SSLDFQVVQPSLPDSNTITQDLKTIPSQNSQIVTSRQIQVNISDFEGHSNPEGTPVFADR
LPEKMKTPLSAFSEKLSSDAVTQITTESPEKTLFSSEIFINAEDRGHEIIEPGNQKLRKA
PVKFASSSSVQQVTFSRGTDGQPLLLPYKPSGSTKMYYVPQLRQIPPSPDSKSDTTVESS
HSGSNDAIAPDFPAQVLGTRDDDLSATVNIKHKEGIYSKRVVTKASLPVGEKPLQNENAD
ASVQVLITGDENLSDKKQQEIHSTRAVTEAAQAKEKESLQKDTADSSAAAAAEHSAQVGD
PEMKNLPDTKAITQKEEIHRKKTVPEEAWPNNKESLQINIEESECHSEFENTTRSVFRSA
KFYIHHPVHLPSDQDICHESLGKSVFMRHSWKDFFQHHPDKHREHMCLPLPYQNMDKTKT
DYTRIKSLSINVNLGNKEVMDTTKSQVRDYPKHNGQISDPQRDQKVTPEQTTQHTVSLNE
LWNKYRERQRQQRQPELGDRKELSLVDRLDRLAKILQNPITHSLQVSESTHDDSRGERSV
KEWSGRQQQRNKLQKKKRFKSLEKSHKNTGELKKSKVLSHHRAGRSNQIKIEQIKFDKYI
LSKQPGFNYISNTSSDCRPSEESELLTDTTTNILSGTTSTVESDILTQTDREVALHERSS
SVSTIDTARLIQAFGHERVCLSPRRIKLYSSITNQQRRYLEKRSKHSKKVLNTGHPLVTS
EHTRRRHIQVANHVISSDSISSSASSFLSSNSTFCNKQNVHMLNKGIQAGNLEIVNGAKK
HTRDVGITFPTPSSSEAKLEENSDVTSWSEEKREEKMLFTGYPEDRKLKKNKKNSHEGVS
WFVPVENVESRSKKENVPNTCGPGISWFEPITKTRPWREPLREQNCQGQHLDGRGYLAGP
GREAGRDLLRPFVRATLQESLQFHRPDFISRSGERIKRLKLIVQERKLQSMLQTERDALF
NIDRERQGHQNRMCPLPKRVFLAIQKNKPISKKEMIQRSKRIYEQLPEVQKKREEEKRKS
EYKSYRLRAQLYKKRVTNQLLGRK
VPWD
Sequence length 4168
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  Reactome
    Regulation of PLK1 Activity at G2/M Transition
Loss of Nlp from mitotic centrosomes
Recruitment of mitotic centrosome proteins and complexes
Loss of proteins required for interphase microtubule organization from the centrosome
Recruitment of NuMA to mitotic centrosomes
Anchoring of the basal body to the plasma membrane
AURKA Activation by TPX2
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
63
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Abnormality of the eye Pathogenic rs2103791192 RCV001814434
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
ALMS1-related disorder Likely pathogenic; Pathogenic rs758016217, rs2466112542, rs2466445896, rs2466097572, rs2104104085, rs761292021, rs1412574975 RCV003417032
RCV003412420
RCV003416677
RCV003403024
RCV003414263
View all (3 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Alstrom syndrome Pathogenic; Likely pathogenic rs568037602, rs1181992959, rs2103787360, rs2104189157, rs1671310097, rs2103734661, rs2104058704, rs1169223296, rs757131983, rs2104060044, rs2103701996, rs2103714765, rs2103734325, rs2103771067, rs2103772743
View all (727 more)
RCV001335703
RCV001375482
RCV001376207
RCV001376523
RCV001379006
View all (758 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Bardet-Biedl syndrome Pathogenic; Likely pathogenic rs387906312, rs2466101466, rs1473611414, rs747747269, rs1672034468 RCV005624668
RCV003222509
RCV003222006
RCV005626365
RCV001328236
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary Conflicting classifications of pathogenicity ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ANOREXIA NERVOSA GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acanthosis Nigricans Acanthosis Nigricans HPO_DG
★☆☆☆☆
Found in Text Mining only
Adult Hodgkin Lymphoma Hodgkin Lymphoma BEFREE 28135309
★☆☆☆☆
Found in Text Mining only
Alopecia Alopecia HPO_DG
★☆☆☆☆
Found in Text Mining only
Alstrom Syndrome Alstrom Syndrome BEFREE 11941369, 11941370, 16000322, 16720663, 17206865, 17594715, 17850632, 18154657, 18654604, 19440062, 20381594, 20514046, 20844083, 21135875, 21897446
View all (28 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Alstrom Syndrome Alstrom Syndrome CLINGEN_DG 11941369, 11941370, 16000322, 21071598, 27523285
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Alstrom Syndrome Alstrom Syndrome CLINVAR_DG 11941369, 11941370, 15689433, 16720663, 17594715, 18038714, 21157496, 22447358, 22555271, 22773737, 22876109, 24462884, 25296579, 25706677, 25846608
View all (8 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Alstrom Syndrome Alstrom Syndrome GENOMICS_ENGLAND_DG 11941370, 15689433, 17850632, 22773737, 25846608, 9921899
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Alstrom Syndrome Alstrom syndrome Pubtator 19279085, 19515241, 20381594, 20844083, 21541333, 21877133, 21897446, 22447358, 22773737, 22876109, 23188138, 23652376, 24049434, 24319333, 24690487
View all (30 more)
Associate
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Alstrom Syndrome Alstrom Syndrome CTD_human_DG 22447358
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Alstrom Syndrome Orphanet
★☆☆☆☆
Found in Text Mining only