WDR19 WD repeat domain 19 [Homo sapiens (human)] - Gene

Summary

Official Symbol: WDR19provided by HGNC
Official Full Name: WD repeat domain 19provided by HGNC
Primary source: HGNC:HGNC:18340
See related: Ensembl:ENSG00000157796 MIM:608151; AllianceGenome:HGNC:18340
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: ATD5; CED4; DYF-2; FAP66; ORF26; Oseg6; PWDMP; SRTD5; CFAP66; IFT144; NPHP13; SPGF72
Summary: The protein encoded by this gene is a member of the WD (tryptophan-aspartic acid) repeat family, which is a large family of structurally-related proteins known to participate in a wide range of cellular processes. Each WD repeat typically contains about 40 amino acids that are usually bracketed by glycine-histidine and tryptophan-aspartic acid (WD) dipeptides. This protein contains six WD repeats, three transmembrane domains, and a clathrin heavy-chain repeat. Mutations in this gene have been described in individuals with a wide range of disorders affecting function of the cilium. These disorders are known as ciliopathies, and include Jeune syndrome, Sensenbrenner syndromes, Senior-Loken syndrome, combined or isolated nephronophthisis (NPHP), and retinitis pigmentosa (RP). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
Expression: Broad expression in thyroid (RPKM 9.7), testis (RPKM 8.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4p14

Exon count:: 37

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (39182529..39285810)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (39152167..39255444)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (39184149..39287430)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Identification of the primary ciliary proteins IFT38 and IFT144 to enhance serum-mediated YAP activation and cell proliferation.
Title: Identification of the primary ciliary proteins IFT38 and IFT144 to enhance serum-mediated YAP activation and cell proliferation.
Stargardt-like Clinical Characteristics and Disease Course Associated with Variants in the WDR19 Gene.
Title: Stargardt-like Clinical Characteristics and Disease Course Associated with Variants in the WDR19 Gene.
Molecular basis of ciliary defects caused by compound heterozygous IFT144/WDR19 mutations found in cranioectodermal dysplasia.
Title: Molecular basis of ciliary defects caused by compound heterozygous IFT144/WDR19 mutations found in cranioectodermal dysplasia.
A novel homozygous mutation in WDR19 induces disorganization of microtubules in sperm flagella and nonsyndromic asthenoteratospermia.
Title: A novel homozygous mutation in WDR19 induces disorganization of microtubules in sperm flagella and nonsyndromic asthenoteratospermia.
Case Reports: that WDR19 mutations can cause dysplastic kidney in addition to nephronophthisis in infants with Sensenbrenner syndrome.
Title: Diversity of renal phenotypes in patients with WDR19 mutations: Two case reports.
Nephronophthisis 13 (Autosomal Recessive Polycystic Kidney Disease) is associated with mutations in the WDR19 gene.Caroli disease is a major extra-renal phenotype associated with mutations in WDR19 in the Korean population.
Title: Nephronophthisis 13: implications of its association with Caroli disease and altered intracellular localization of WDR19 in the kidney.
WDR19 mutations can cause a broad spectrum of ciliopathies that extends to Jeune and Sensenbrenner syndromes, RP and renal NPHP-like phenotypes
Title: Mutations in WDR19 encoding the intraflagellar transport component IFT144 cause a broad spectrum of ciliopathies.
Mutations in WDR19 gene is associated with Caroli disease.
Title: Identification of 99 novel mutations in a worldwide cohort of 1,056 patients with a nephronophthisis-related ciliopathy.
WDR19: an ancient, retrograde, intraflagellar ciliary protein is mutated in autosomal recessive retinitis pigmentosa and in Senior-Loken syndrome.
Title: WDR19: an ancient, retrograde, intraflagellar ciliary protein is mutated in autosomal recessive retinitis pigmentosa and in Senior-Loken syndrome.
Ciliopathies with skeletal anomalies and renal insufficiency due to mutations in the IFT-A gene WDR19
Title: Ciliopathies with skeletal anomalies and renal insufficiency due to mutations in the IFT-A gene WDR19.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Asphyxiating thoracic dystrophy 5 MedGen: C3280598 OMIM: 614376 GeneReviews: Not available	not available
Cranioectodermal dysplasia 4 MedGen: C3280616 OMIM: 614378 GeneReviews: Cranioectodermal Dysplasia	not available
Nephronophthisis 13 MedGen: C3280612 OMIM: 614377 GeneReviews: Nephronophthisis-Related Ciliopathies	not available
Senior-Loken syndrome 8 MedGen: C4225376 OMIM: 616307 GeneReviews: Not available	not available
Spermatogenic failure 72 MedGen: C5676980 OMIM: 619867 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Heritability and genetic association analysis of cognition in the&#x000a0;Diabetes Heart Study. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-68104 (e-PCR)
- UniSTS:22062

D4S642 (e-PCR)
- UniSTS:148295

D17S1238 (e-PCR)
- UniSTS:149851

D12S1332 (e-PCR)
- UniSTS:48481

D1S1423 (e-PCR)
- UniSTS:149619

D1S1425 (e-PCR)
- UniSTS:149621

RH98905 (e-PCR)
- UniSTS:92819

NoName (e-PCR)
- UniSTS:489949

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cell morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in cilium assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in cilium assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in digestive system development	IEA Inferred from Electronic Annotation more info
involved_in ear morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in embryonic camera-type eye development	IEA Inferred from Electronic Annotation more info
involved_in embryonic cranial skeleton morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in embryonic limb morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in gonad development	IEA Inferred from Electronic Annotation more info
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
involved_in intraciliary retrograde transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within intraciliary retrograde transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intraciliary retrograde transport	NAS Non-traceable Author Statement more info	PubMed
involved_in myotome development	IEA Inferred from Electronic Annotation more info
involved_in nervous system process	IEA Inferred from Electronic Annotation more info
involved_in protein localization to ciliary membrane	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein-containing complex assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in receptor clustering	IEA Inferred from Electronic Annotation more info
involved_in smoothened signaling pathway involved in dorsal/ventral neural tube patterning	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in ciliary tip	TAS Traceable Author Statement more info
is_active_in cilium	IBA Inferred from Biological aspect of Ancestor more info
located_in cilium	NAS Non-traceable Author Statement more info	PubMed
located_in cilium	TAS Traceable Author Statement more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
part_of intraciliary transport particle A	IBA Inferred from Biological aspect of Ancestor more info
part_of intraciliary transport particle A	IDA Inferred from Direct Assay more info	PubMed
part_of intraciliary transport particle A	IPI Inferred from Physical Interaction more info	PubMed
located_in motile cilium	ISS Inferred from Sequence or Structural Similarity more info
located_in non-motile cilium	ISS Inferred from Sequence or Structural Similarity more info
located_in photoreceptor connecting cilium	ISS Inferred from Sequence or Structural Similarity more info
located_in photoreceptor outer segment	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: WD repeat-containing protein 19

Names: WD repeat membrane protein PWDMP; intraflagellar transport 144 homolog

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_031813.1 RefSeqGene

Range

5126..108407

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001317924.2 → NP_001304853.1 WD repeat-containing protein 19 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in its 5' UTR compared to variant 1. This variant represents translation initiation at a downstream start codon compared to variant 1; the 5'-most initiation codon, as used in variant 1, is associated with a truncated ORF that would render the transcript a candidate for nonsense-mediated decay (NMD). Leaky scanning may allow translation initiation at the downstream start codon to encode an isoform (2) that has a shorter N-terminus, compared to isoform 1

Source sequence(s)

AK225588, AK294730

UniProtKB/TrEMBL

B4DGR6, B4E286

Conserved Domains (8) summary

COG0457
Location:702 → 982

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

COG2319
Location:2 → 186

WD40; WD40 repeat [General function prediction only]

COG5290
Location:672 → 770

COG5290; IkappaB kinase complex, IKAP component [Transcription]

sd00006
Location:619 → 643

TPR; TPR repeat [structural motif]

pfam12773
Location:1093 → 1135

DZR; Double zinc ribbon

pfam15911
Location:348 → 404

WD40_3; WD domain, G-beta repeat

sd00039
Location:73 → 112

7WD40; WD40 repeat [structural motif]

cl02567
Location:114 → 186

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_025132.4 → NP_079408.3 WD repeat-containing protein 19 isoform 1

See identical proteins and their annotated locations for NP_079408.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AB046858, AK026780, AK122908, AY029257, BC032578

Consensus CDS

CCDS47042.1

UniProtKB/Swiss-Prot

B5MEF2, Q8N5B4, Q8NEZ3, Q9H5S0, Q9HCD4

UniProtKB/TrEMBL

B4E286

Related

ENSP00000382717.3, ENST00000399820.8

Conserved Domains (8) summary

COG0457
Location:862 → 1142

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

COG2319
Location:19 → 345

WD40; WD40 repeat [General function prediction only]

COG5290
Location:832 → 930

COG5290; IkappaB kinase complex, IKAP component [Transcription]

sd00006
Location:779 → 803

TPR; TPR repeat [structural motif]

pfam12773
Location:1253 → 1295

DZR; Double zinc ribbon

pfam15911
Location:508 → 564

WD40_3; WD domain, G-beta repeat

sd00039
Location:57 → 98

7WD40; WD40 repeat [structural motif]

cl02567
Location:26 → 302

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

39182529..39285810

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011513724.2 → XP_011512026.1 WD repeat-containing protein 19 isoform X1

UniProtKB/TrEMBL

B4E286

Conserved Domains (8) summary

COG0457
Location:866 → 1146

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

COG2319
Location:19 → 345

WD40; WD40 repeat [General function prediction only]

COG5290
Location:836 → 934

COG5290; IkappaB kinase complex, IKAP component [Transcription]

sd00006
Location:783 → 807

TPR; TPR repeat [structural motif]

pfam12773
Location:1257 → 1299

DZR; Double zinc ribbon

pfam15911
Location:508 → 564

WD40_3; WD domain, G-beta repeat

sd00039
Location:57 → 98

7WD40; WD40 repeat [structural motif]

cl02567
Location:26 → 302

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_011513725.3 → XP_011512027.1 WD repeat-containing protein 19 isoform X2

UniProtKB/TrEMBL

B4E286

Conserved Domains (8) summary

COG0457
Location:844 → 1124

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

COG2319
Location:32 → 323

WD40; WD40 repeat [General function prediction only]

COG5290
Location:814 → 912

COG5290; IkappaB kinase complex, IKAP component [Transcription]

sd00006
Location:761 → 785

TPR; TPR repeat [structural motif]

pfam12773
Location:1235 → 1277

DZR; Double zinc ribbon

pfam15911
Location:486 → 542

WD40_3; WD domain, G-beta repeat

sd00039
Location:35 → 76

7WD40; WD40 repeat [structural motif]

cl02567
Location:32 → 324

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_047416030.1 → XP_047271986.1 WD repeat-containing protein 19 isoform X3
XM_047416031.1 → XP_047271987.1 WD repeat-containing protein 19 isoform X4
XM_047416032.1 → XP_047271988.1 WD repeat-containing protein 19 isoform X5
XM_047416034.1 → XP_047271990.1 WD repeat-containing protein 19 isoform X7
XM_047416035.1 → XP_047271991.1 WD repeat-containing protein 19 isoform X8
XM_047416033.1 → XP_047271989.1 WD repeat-containing protein 19 isoform X6