Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	54903
Gene name Gene Name - the full gene name approved by the HGNC.	MKS transition zone complex subunit 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	MKS1
Synonyms (NCBI Gene) Gene synonyms aliases	BBS13, JBTS28, MES, MKS, POC12
Chromosome Chromosome number	17
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	17q22
Summary Summary of gene provided in NCBI Entrez Gene.	The protein encoded by this gene localizes to the basal body and is required for formation of the primary cilium in ciliated epithelial cells. Mutations in this gene result in Meckel syndrome type 1 and in Bardet-Biedl syndrome type 13. Multiple transcrip

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SNP ID	Visualize variation	Clinical significance	Consequence
rs62636631	C>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, non coding transcript variant, 5 prime UTR variant, coding sequence variant
rs111315726	C>T	Conflicting-interpretations-of-pathogenicity, benign-likely-benign	Missense variant, coding sequence variant, intron variant, genic downstream transcript variant
rs137853105	A>C	Pathogenic, uncertain-significance	Missense variant, coding sequence variant, intron variant, genic downstream transcript variant
rs142805406	G>A,C	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant, non coding transcript variant
rs144635826	T>C	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, genic downstream transcript variant, synonymous variant, non coding transcript variant, missense variant
rs199684837	G>A,C	Conflicting-interpretations-of-pathogenicity, likely-benign	Intron variant, synonymous variant, non coding transcript variant, coding sequence variant
rs199874059	C>T	Likely-pathogenic, pathogenic-likely-pathogenic	Splice donor variant
rs199910690	C>T	Conflicting-interpretations-of-pathogenicity, pathogenic	3 prime UTR variant, missense variant, synonymous variant, non coding transcript variant, genic downstream transcript variant, coding sequence variant
rs200149256	C>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Intron variant, missense variant, non coding transcript variant, coding sequence variant
rs200156751	G>A	Conflicting-interpretations-of-pathogenicity, likely-benign	Intron variant
rs200865108	A>G	Likely-pathogenic, conflicting-interpretations-of-pathogenicity	Intron variant, downstream transcript variant, genic downstream transcript variant, coding sequence variant, missense variant, non coding transcript variant
rs201137386	C>T	Conflicting-interpretations-of-pathogenicity	Intron variant
rs201619500	C>T	Benign-likely-benign, conflicting-interpretations-of-pathogenicity, uncertain-significance	Intron variant, downstream transcript variant, genic downstream transcript variant, coding sequence variant, missense variant, non coding transcript variant
rs201845569	T>C	Conflicting-interpretations-of-pathogenicity, likely-benign	Non coding transcript variant, coding sequence variant, missense variant
rs201933838	C>T	Likely-pathogenic, pathogenic	Intron variant, splice donor variant
rs201961765	G>A,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Non coding transcript variant, synonymous variant, coding sequence variant, missense variant
rs368535131	C>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Synonymous variant, genic downstream transcript variant, coding sequence variant, missense variant, non coding transcript variant
rs372554696	C>T	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, missense variant
rs375046501	A>G	Conflicting-interpretations-of-pathogenicity	Intron variant
rs376823839	G>A	Conflicting-interpretations-of-pathogenicity	Intron variant
rs386834041	G>A,C	Likely-pathogenic	Non coding transcript variant, stop gained, coding sequence variant, missense variant
rs386834042	A>-	Likely-pathogenic	Intron variant, downstream transcript variant, splice donor variant, genic downstream transcript variant
rs386834043	ATGCCATTGGGACAGCCTCAGGTTTCTGC>-	Pathogenic, conflicting-interpretations-of-pathogenicity	Intron variant, genic downstream transcript variant
rs386834044	->CCTG	Likely-pathogenic, pathogenic	Intron variant, frameshift variant, coding sequence variant, genic downstream transcript variant
rs386834045	C>T	Likely-pathogenic	Intron variant, missense variant, coding sequence variant, genic downstream transcript variant
rs386834047	AG>-	Likely-pathogenic	Non coding transcript variant, stop gained, coding sequence variant, 5 prime UTR variant
rs386834048	C>T	Likely-pathogenic, pathogenic, uncertain-significance	Non coding transcript variant, synonymous variant, coding sequence variant, 5 prime UTR variant
rs386834049	G>A	Likely-pathogenic	Intron variant, stop gained, coding sequence variant, 5 prime UTR variant, non coding transcript variant
rs386834050	G>A	Likely-pathogenic, pathogenic	Non coding transcript variant, intron variant, stop gained, coding sequence variant
rs386834053	C>T	Likely-pathogenic, uncertain-significance	Intron variant, coding sequence variant, missense variant
rs587777804	AAG>-	Pathogenic	Coding sequence variant, non coding transcript variant, inframe deletion
rs730882120	T>C	Pathogenic, uncertain-significance	Coding sequence variant, downstream transcript variant, intron variant, missense variant, non coding transcript variant, genic downstream transcript variant
rs754279998	GAG>-	Likely-pathogenic, pathogenic	Coding sequence variant, inframe deletion, non coding transcript variant
rs754404940	G>A	Conflicting-interpretations-of-pathogenicity	Intron variant
rs756102768	C>G,T	Likely-pathogenic	Splice donor variant
rs756368560	C>A,T	Likely-pathogenic	Splice donor variant
rs756853299	G>A	Likely-pathogenic	Coding sequence variant, stop gained, intron variant, non coding transcript variant
rs762668200	->C	Pathogenic	Coding sequence variant, splice acceptor variant, genic downstream transcript variant, intron variant
rs766392300	G>A,C,T	Pathogenic	Coding sequence variant, intron variant, synonymous variant, missense variant, genic downstream transcript variant, downstream transcript variant, non coding transcript variant
rs773036963	T>A	Pathogenic	Splice acceptor variant
rs773269657	C>A	Likely-pathogenic	Non coding transcript variant, intron variant, downstream transcript variant, genic downstream transcript variant, synonymous variant, coding sequence variant
rs773684291	G>A,C	Pathogenic, uncertain-significance, likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs775043799	->G	Likely-pathogenic	5 prime UTR variant, non coding transcript variant, frameshift variant, coding sequence variant
rs775169308	C>A,G,T	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, synonymous variant, coding sequence variant
rs779953982	G>A	Uncertain-significance, likely-pathogenic	Missense variant, intron variant, non coding transcript variant, coding sequence variant
rs786204222	A>C,G	Uncertain-significance, pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant, non coding transcript variant
rs786205508	G>A	Pathogenic, likely-pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs794727070	T>G	Likely-pathogenic, pathogenic	Splice acceptor variant
rs797045706	G>A	Likely-pathogenic, pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs863225204	->G	Pathogenic	Frameshift variant, genic downstream transcript variant, coding sequence variant, non coding transcript variant
rs863225206	G>-	Pathogenic	Frameshift variant, coding sequence variant, 5 prime UTR variant, non coding transcript variant
rs863225207	T>A	Pathogenic	Genic downstream transcript variant, splice acceptor variant
rs863225208	C>T	Pathogenic	Missense variant, coding sequence variant, intron variant
rs863225209	->G	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs863225210	G>A	Pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs865870355	G>-	Likely-pathogenic	Frameshift variant, genic downstream transcript variant, coding sequence variant, intron variant, non coding transcript variant, downstream transcript variant
rs886038203	T>C	Pathogenic	Genic downstream transcript variant, splice acceptor variant
rs886038204	C>A	Pathogenic	Genic downstream transcript variant, splice donor variant
rs886039803	A>T	Pathogenic	Splice donor variant
rs1114167302	C>A	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant, 5 prime UTR variant
rs1376664664	A>C,G	Likely-pathogenic	Intron variant, splice donor variant
rs1488635637	T>C,G	Likely-pathogenic, pathogenic	Splice acceptor variant
rs1555596845	GTGACAGTGCCTGTGGTCTCTGTGCGGAG>-	Likely-pathogenic	Frameshift variant, intron variant, genic downstream transcript variant, coding sequence variant
rs1555596943	T>C	Likely-pathogenic	Intron variant, splice acceptor variant, genic downstream transcript variant
rs1555599412	C>A	Likely-pathogenic, pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs1555600644	ATTATAATACATCAAACTTTTGCTTCTGTAACTGTTTAATCAAATCAGTTCTACAGAACTGATGCTATCTGACATGTTTTCATAACCAACACTAAACTAATGAATGGCAGGGGAACCAAGAACATTAGAGCTAAAAGGAACCA>-	Pathogenic	Intron variant
rs1567796331	C>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant

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miRTarBase ID	miRNA	Experiments
MIRT1150488	hsa-miR-3613-3p	CLIP-seq
MIRT1150489	hsa-miR-4434	CLIP-seq
MIRT1150490	hsa-miR-4516	CLIP-seq
MIRT1150491	hsa-miR-4531	CLIP-seq
MIRT1150492	hsa-miR-4773	CLIP-seq
MIRT1150493	hsa-miR-495	CLIP-seq
MIRT1150494	hsa-miR-922	CLIP-seq
MIRT2042857	hsa-miR-1229	CLIP-seq
MIRT2042858	hsa-miR-2467-3p	CLIP-seq
MIRT2042859	hsa-miR-2682	CLIP-seq
MIRT2042860	hsa-miR-298	CLIP-seq
MIRT2042861	hsa-miR-3158-5p	CLIP-seq
MIRT2042862	hsa-miR-3667-3p	CLIP-seq
MIRT2042863	hsa-miR-3667-5p	CLIP-seq
MIRT2042864	hsa-miR-449c	CLIP-seq
MIRT2042865	hsa-miR-4725-5p	CLIP-seq
MIRT2042866	hsa-miR-504	CLIP-seq
MIRT2042867	hsa-miR-940	CLIP-seq
MIRT2272494	hsa-miR-3065-3p	CLIP-seq
MIRT2272495	hsa-miR-512-5p	CLIP-seq
MIRT2272496	hsa-miR-621	CLIP-seq
MIRT2454156	hsa-miR-4323	CLIP-seq
MIRT2454157	hsa-miR-4714-3p	CLIP-seq
MIRT2454158	hsa-miR-545	CLIP-seq
MIRT2042857	hsa-miR-1229	CLIP-seq
MIRT2571395	hsa-miR-1237	CLIP-seq
MIRT2571396	hsa-miR-1248	CLIP-seq
MIRT2571397	hsa-miR-133a	CLIP-seq
MIRT2571398	hsa-miR-133b	CLIP-seq
MIRT2571399	hsa-miR-208a	CLIP-seq
MIRT2571400	hsa-miR-208b	CLIP-seq
MIRT2571401	hsa-miR-3174	CLIP-seq
MIRT2571402	hsa-miR-3609	CLIP-seq
MIRT2571403	hsa-miR-3658	CLIP-seq
MIRT2042862	hsa-miR-3667-3p	CLIP-seq
MIRT2042863	hsa-miR-3667-5p	CLIP-seq
MIRT2571404	hsa-miR-3672	CLIP-seq
MIRT2571405	hsa-miR-432	CLIP-seq
MIRT2571406	hsa-miR-4438	CLIP-seq
MIRT2571407	hsa-miR-4450	CLIP-seq
MIRT2571408	hsa-miR-4505	CLIP-seq
MIRT2571409	hsa-miR-4667-5p	CLIP-seq
MIRT2571410	hsa-miR-4700-5p	CLIP-seq
MIRT2571411	hsa-miR-4731-5p	CLIP-seq
MIRT2571412	hsa-miR-488	CLIP-seq
MIRT2571413	hsa-miR-499-5p	CLIP-seq
MIRT2571414	hsa-miR-513a-5p	CLIP-seq
MIRT2571415	hsa-miR-548ah	CLIP-seq
MIRT2571416	hsa-miR-548t	CLIP-seq
MIRT2571417	hsa-miR-7	CLIP-seq
MIRT2571418	hsa-miR-9	CLIP-seq
MIRT2042857	hsa-miR-1229	CLIP-seq
MIRT2571399	hsa-miR-208a	CLIP-seq
MIRT2571400	hsa-miR-208b	CLIP-seq
MIRT2571403	hsa-miR-3658	CLIP-seq
MIRT2042863	hsa-miR-3667-5p	CLIP-seq
MIRT2571404	hsa-miR-3672	CLIP-seq
MIRT2571406	hsa-miR-4438	CLIP-seq
MIRT2571407	hsa-miR-4450	CLIP-seq
MIRT2571408	hsa-miR-4505	CLIP-seq
MIRT2571409	hsa-miR-4667-5p	CLIP-seq
MIRT2571410	hsa-miR-4700-5p	CLIP-seq
MIRT2571411	hsa-miR-4731-5p	CLIP-seq
MIRT2571413	hsa-miR-499-5p	CLIP-seq
MIRT2571414	hsa-miR-513a-5p	CLIP-seq

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GO ID	Ontology	Definition	Evidence	Reference
GO:0001843	Process	Neural tube closure	IEA
GO:0003271	Process	Smoothened signaling pathway involved in regulation of secondary heart field cardioblast proliferation	IEA
GO:0005515	Function	Protein binding	IPI	17185389, 19515853, 26595381, 26638075, 32726168, 33961781
GO:0005654	Component	Nucleoplasm	IDA
GO:0005730	Component	Nucleolus	IDA
GO:0005737	Component	Cytoplasm	IDA	17185389
GO:0005737	Component	Cytoplasm	IEA
GO:0005813	Component	Centrosome	IDA	19208769, 19515853
GO:0005813	Component	Centrosome	IEA
GO:0005814	Component	Centriole	IEA
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0005929	Component	Cilium	IEA
GO:0007368	Process	Determination of left/right symmetry	IEA
GO:0008589	Process	Regulation of smoothened signaling pathway	IEA
GO:0010669	Process	Epithelial structure maintenance	IEA
GO:0016020	Component	Membrane	IEA
GO:0030030	Process	Cell projection organization	IEA
GO:0035869	Component	Ciliary transition zone	IEA
GO:0036038	Component	MKS complex	IBA
GO:0036038	Component	MKS complex	IEA
GO:0036038	Component	MKS complex	ISS
GO:0036064	Component	Ciliary basal body	IDA	19208769, 19515853
GO:0042733	Process	Embryonic digit morphogenesis	IEA
GO:0042995	Component	Cell projection	IEA
GO:0044458	Process	Motile cilium assembly	IEA
GO:0048706	Process	Embryonic skeletal system development	IEA
GO:0048754	Process	Branching morphogenesis of an epithelial tube	IEA
GO:0060122	Process	Inner ear receptor cell stereocilium organization	IEA
GO:0060271	Process	Cilium assembly	IBA
GO:0060271	Process	Cilium assembly	IEA
GO:0060271	Process	Cilium assembly	IMP	19515853
GO:0060271	Process	Cilium assembly	ISS
GO:0060322	Process	Head development	IEA
GO:0060411	Process	Cardiac septum morphogenesis	IEA
GO:0060828	Process	Regulation of canonical Wnt signaling pathway	IEA
GO:0061009	Process	Common bile duct development	IEA
GO:1905515	Process	Non-motile cilium assembly	IEA
GO:1990403	Process	Embryonic brain development	IEA
GO:2000095	Process	Regulation of Wnt signaling pathway, planar cell polarity pathway	IEA

MIM	HGNC	e!Ensembl
609883	7121	ENSG00000011143

Protein

UniProt ID

Q9NXB0

Protein name

Tectonic-like complex member MKS1 (Meckel syndrome type 1 protein)

Protein function

Component of the tectonic-like complex, a complex localized at the transition zone of primary cilia and acting as a barrier that prevents diffusion of transmembrane proteins between the cilia and plasma membranes. Involved in centrosome migratio

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF07162	B9-C2	313 → 493	Ciliary basal body-associated, B9 protein	Domain

Sequence

MAETVWSTDTGEAVYRSRDPVRNLRLRVHLQRITSSNFLHYQPAAELGKDLIDLATFRPQ
PTASGHRPEEDEEEEIVIGWQEKLFSQFEVDLYQNETACQSPLDYQYRQEILKLENSGGK
KNRRIFTYTDSDRYTNLEEHCQRMTTAASEVPSFLVERMANVRRRRQDRRGMEGGILKSR
IVTWEPSEEFVRNNHVINTPLQTMHIMADLGPYKKLGYKKYEHVLCTLKVDSNGVITVKP
DFTGLKGPYRIETEGEKQELWKYTIDNVSPHAQPEEEERERRVFKDLYGRHKEYLSSLVG
TDFEMTVPGALRLFVNGEVVSAQGYEYDNLYVHFFVELPTAHWSSPAFQQLSGVTQTCTT
KSLAMDKVAHFSYPFTFEAFFLHEDESSDALPEWPVLYCEVLSLDFWQRYRVEGYGAVVL
PATPGSHTLTVSTWRPVELGTVAELRRFFIGGSLELEDLSYVRIPGSFKGERLSRFGLRT
ETTGTVTFRLHCLQQSRAFMESSSLQKRMRSVLDRLEGFSQQSSIHNVLEAFRRARRRMQ
EARESLPQDLVSPSGTLVS

Sequence length

559

Interactions

View interactions

	Reactome
			Hedgehog 'off' state Anchoring of the basal body to the plasma membrane

Show/Hide Causal Diseases (5)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Bardet-Biedl Syndrome	bardet-biedl syndrome 13	rs865870355, rs756368560, rs386834050, rs375170572, rs794727070, rs903778224, rs775043799, rs201933838, rs797045706, rs756853299, rs386834044, rs386834051, rs762668200, rs386834046, rs1488635637 View all (4 more)	N/A
Cerebellar vermis agenesis	familial aplasia of the vermis	rs863225209, rs863225206, rs1555600644, rs386834044, rs863225205, rs863225207, rs1114167302, rs863225204, rs863225210, rs386834043, rs754279998, rs863225208	N/A
Joubert Syndrome	joubert syndrome 28	rs865870355, rs375170572, rs386834044, rs775043799, rs886038203, rs886038204, rs386834043, rs754279998	N/A
Meckel syndrome	Meckel syndrome, type 1	rs386834049, rs375170572, rs386834042, rs386834050, rs756368560, rs386834044, rs865870355, rs775043799, rs201933838, rs797045706, rs386834051, rs730880323, rs386834045, rs762668200, rs386834052 View all (7 more)	N/A
Meckel-Gruber Syndrome	meckel-gruber syndrome	rs886039803, rs786205508	N/A

Show/Hide Unknown Diseases (5)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Joubert Syndrome With Ocular Defect	Joubert syndrome with ocular defect	N/A	N/A	GenCC
Microcephaly	microcephaly	N/A	N/A	ClinVar
Optic Atrophy	optic atrophy	N/A	N/A	ClinVar
Peripheral Neuropathy	peripheral neuropathy	N/A	N/A	ClinVar
retinal dystrophy	Retinal dystrophy	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (5)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Agenesis of Cerebellar Vermis	Associate	17160906, 24886560, 30055837, 36788019, 37131188
Apraxia oculomotor Cogan type	Associate	37131188
Bardet Biedl Syndrome	Associate	19797195, 20177705, 24608809
Ciliopathies	Associate	21068128, 24886560
Meckel syndrome type 1	Associate	17160906, 21493627, 24886560

MKS1 (MKS transition zone complex subunit 1)