IFT172 intraflagellar transport 172 [Homo sapiens (human)] - Gene

Summary

Official Symbol: IFT172provided by HGNC
Official Full Name: intraflagellar transport 172provided by HGNC
Primary source: HGNC:HGNC:30391
See related: Ensembl:ENSG00000138002 MIM:607386; AllianceGenome:HGNC:30391
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: SLB; wim; RP71; BBS20; osm-1; NPHP17; SRTD10
Summary: This gene encodes a subunit of the intraflagellar transport subcomplex IFT-B. Subcomplexes IFT-A and IFT-B are necessary for ciliary assembly and maintenance. Mutations in this gene have been associated with skeletal ciliopathies, with or without polydactyly, such as such short-rib thoracic dysplasias 1, 9 or 10. [provided by RefSeq, Mar 2014]
Expression: Broad expression in testis (RPKM 10.6), ovary (RPKM 4.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2p23.3

Exon count:: 53

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (27444377..27489743, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (27486730..27532099, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (27667244..27712610, complement)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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?

Exome sequencing reveals IFT172 variants in patients with non-syndromic cholestatic liver disease.
Title: Exome sequencing reveals IFT172 variants in patients with non-syndromic cholestatic liver disease.
Novel alterations in IFT172 and KIFAP3 may induce basal cell carcinoma.
Title: Novel alterations in IFT172 and KIFAP3 may induce basal cell carcinoma.
Multimodal imaging of retinitis pigmentosa associated with Mainzer-Saldino syndrome.
Title: Multimodal imaging of retinitis pigmentosa associated with Mainzer-Saldino syndrome.
We found that depletion of IFT172 in rod photoreceptors leads to a rapid degeneration of the retina, with severely reduced electroretinography (ERG) responses by 1 month and complete outer-nuclear layer (ONL) degeneration by 2 months
Title: Ift172 conditional knock-out mice exhibit rapid retinal degeneration and protein trafficking defects.
This is the second report of IFT172 mutations in BBS patients validating IFT172 as the twentieth BBS gene (BBS20).
Title: Identification of a novel mutation confirms the implication of IFT172 (BBS20) in Bardet-Biedl syndrome.
Findings identified mutations in IFT172 that lead to a recessive form of non-syndromic retinitis pigmentosa and Bardet-Biedl syndrome and suggest that the primary IFT172 mutations alone are not sufficient to explain the wide range of phenotypes.
Title: Mutations in IFT172 cause isolated retinal degeneration and Bardet-Biedl syndrome.
We have identified defects in IFT172 as a cause of complex asphyxiating thoracic dystrophy and Mainzer-Saldino syndrome.
Title: Defects in the IFT-B component IFT172 cause Jeune and Mainzer-Saldino syndromes in humans.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Bardet-Biedl syndrome 20 MedGen: C4310707 OMIM: 619471 GeneReviews: Not available	Compare labs
Nephronophthisis MedGen: C0687120 GeneReviews: Nephronophthisis-Related Ciliopathies	Compare labs
Retinitis pigmentosa 71 MedGen: C4225342 OMIM: 616394 GeneReviews: Not available	Compare labs
Short-rib thoracic dysplasia 10 with or without polydactyly MedGen: C3810175 OMIM: 615630 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Common variants in the calcium-sensing receptor gene are associated with total serum calcium levels. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
New loci associated with kidney function and chronic kidney disease. 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

D2S1979 (e-PCR)
- UniSTS:8989

D8S2279 (e-PCR)
- UniSTS:473907

MARC_8083-8084:996688275:1 (e-PCR)
- UniSTS:269889

D1S1423 (e-PCR)
- UniSTS:149619

RH92034 (e-PCR)
- UniSTS:87789

Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
involved_in Notch signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in bone development	IEA Inferred from Electronic Annotation more info
involved_in brain development	IEA Inferred from Electronic Annotation more info
involved_in cilium assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in cilium assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in cilium assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in cytoplasmic microtubule organization	IEA Inferred from Electronic Annotation more info
involved_in dorsal/ventral pattern formation	IEA Inferred from Electronic Annotation more info
involved_in embryonic camera-type eye morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in epidermis development	IEA Inferred from Electronic Annotation more info
involved_in heart looping	IEA Inferred from Electronic Annotation more info
involved_in hindgut development	IEA Inferred from Electronic Annotation more info
involved_in intraciliary anterograde transport	NAS Non-traceable Author Statement more info	PubMed
involved_in intraciliary transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in keratinocyte proliferation	IEA Inferred from Electronic Annotation more info
involved_in left/right axis specification	IEA Inferred from Electronic Annotation more info
involved_in limb development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of keratinocyte proliferation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of smoothened signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in neural tube closure	IEA Inferred from Electronic Annotation more info
involved_in non-motile cilium assembly	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of smoothened signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in protein processing	IEA Inferred from Electronic Annotation more info
involved_in roof of mouth development	IEA Inferred from Electronic Annotation more info
involved_in smoothened signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in spinal cord motor neuron differentiation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in axoneme	IBA Inferred from Biological aspect of Ancestor more info
is_active_in ciliary basal body	IBA Inferred from Biological aspect of Ancestor more info
located_in ciliary tip	TAS Traceable Author Statement more info
located_in cilium	ISS Inferred from Sequence or Structural Similarity more info
located_in cilium	NAS Non-traceable Author Statement more info	PubMed
located_in cilium	TAS Traceable Author Statement more info
located_in extracellular vesicle	HDA more info	PubMed
part_of intraciliary transport particle B	IBA Inferred from Biological aspect of Ancestor more info
part_of intraciliary transport particle B	IPI Inferred from Physical Interaction more info	PubMed
part_of intraciliary transport particle B	ISS Inferred from Sequence or Structural Similarity more info
located_in sperm cytoplasmic droplet	IEA Inferred from Electronic Annotation more info
located_in sperm midpiece	IEA Inferred from Electronic Annotation more info
located_in sperm principal piece	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: intraflagellar transport protein 172 homolog

Names: intraflagellar transport 172 homolog; selective LIM binding factor homolog; wimple 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_034068.1 RefSeqGene

Range

5069..50435

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001410739.1 → NP_001397668.1 intraflagellar transport protein 172 homolog isoform 2

Status: REVIEWED

Source sequence(s)

AC074117

Consensus CDS

CCDS92725.1

UniProtKB/TrEMBL

A0A6Q8PGJ2

Related

ENSP00000502283.1, ENST00000675690.1
NM_015662.3 → NP_056477.1 intraflagellar transport protein 172 homolog isoform 1

See identical proteins and their annotated locations for NP_056477.1

Status: REVIEWED

Source sequence(s)

BC047294, BC137126, DC394416

Consensus CDS

CCDS1755.1

UniProtKB/Swiss-Prot

A5PKZ0, B2RNU5, Q86X44, Q96HW4, Q9UFJ9, Q9UG01, Q9ULP1

Related

ENSP00000260570.3, ENST00000260570.8

Conserved Domains (5) summary

COG2319
Location:17 → 388

WD40; WD40 repeat [General function prediction only]

cd15832
Location:811 → 866

SNAP; TPR repeat [structural motif]

sd00039
Location:20 → 64

7WD40; WD40 repeat [structural motif]

cl02567
Location:17 → 318

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 ...

cl24038
Location:808 → 994

SNAP; Soluble N-ethylmaleimide-sensitive factor (NSF) Attachment Protein family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

27444377..27489743 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047443900.1 → XP_047299856.1 intraflagellar transport protein 172 homolog isoform X3
XM_006711987.2 → XP_006712050.1 intraflagellar transport protein 172 homolog isoform X2

Conserved Domains (5) summary

COG2319
Location:17 → 388

WD40; WD40 repeat [General function prediction only]

cd15832
Location:811 → 866

SNAP; TPR repeat [structural motif]

sd00039
Location:20 → 64

7WD40; WD40 repeat [structural motif]

cl02567
Location:17 → 318

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 ...

cl24038
Location:808 → 994

SNAP; Soluble N-ethylmaleimide-sensitive factor (NSF) Attachment Protein family
XM_006711986.4 → XP_006712049.1 intraflagellar transport protein 172 homolog isoform X1

Related

ENST00000507184.5

Conserved Domains (5) summary

COG2319
Location:1 → 284

WD40; WD40 repeat [General function prediction only]

cd15832
Location:790 → 845

SNAP; TPR repeat [structural motif]

sd00039
Location:2 → 43

7WD40; WD40 repeat [structural motif]

cl02567
Location:1 → 297

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 ...

cl24038
Location:787 → 973

SNAP; Soluble N-ethylmaleimide-sensitive factor (NSF) Attachment Protein family
XM_047443902.1 → XP_047299858.1 intraflagellar transport protein 172 homolog isoform X4
XM_047443901.1 → XP_047299857.1 intraflagellar transport protein 172 homolog isoform X4
XM_047443904.1 → XP_047299860.1 intraflagellar transport protein 172 homolog isoform X8
XM_011532759.3 → XP_011531061.1 intraflagellar transport protein 172 homolog isoform X7

Conserved Domains (2) summary

cd15832
Location:291 → 346

SNAP; TPR repeat [structural motif]

cl24038
Location:288 → 474

SNAP; Soluble N-ethylmaleimide-sensitive factor (NSF) Attachment Protein family
XM_011532760.3 → XP_011531062.1 intraflagellar transport protein 172 homolog isoform X9

Conserved Domains (2) summary

cd15832
Location:166 → 221

SNAP; TPR repeat [structural motif]

cl24038
Location:163 → 349

SNAP; Soluble N-ethylmaleimide-sensitive factor (NSF) Attachment Protein family
XM_047443903.1 → XP_047299859.1 intraflagellar transport protein 172 homolog isoform X6
XM_011532758.2 → XP_011531060.1 intraflagellar transport protein 172 homolog isoform X5

Conserved Domains (5) summary

COG2319
Location:17 → 388

WD40; WD40 repeat [General function prediction only]

cd15832
Location:811 → 866

SNAP; TPR repeat [structural motif]

sd00039
Location:20 → 64

7WD40; WD40 repeat [structural motif]

cl02567
Location:17 → 318

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 ...

cl24038
Location:808 → 994

SNAP; Soluble N-ethylmaleimide-sensitive factor (NSF) Attachment Protein family

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

27486730..27532099 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054341345.1 → XP_054197320.1 intraflagellar transport protein 172 homolog isoform X3
XM_054341344.1 → XP_054197319.1 intraflagellar transport protein 172 homolog isoform X2
XM_054341343.1 → XP_054197318.1 intraflagellar transport protein 172 homolog isoform X1
XM_054341347.1 → XP_054197322.1 intraflagellar transport protein 172 homolog isoform X4
XM_054341346.1 → XP_054197321.1 intraflagellar transport protein 172 homolog isoform X4
XM_054341351.1 → XP_054197326.1 intraflagellar transport protein 172 homolog isoform X8
XM_054341350.1 → XP_054197325.1 intraflagellar transport protein 172 homolog isoform X7
XM_054341352.1 → XP_054197327.1 intraflagellar transport protein 172 homolog isoform X9
XM_054341349.1 → XP_054197324.1 intraflagellar transport protein 172 homolog isoform X6
XM_054341348.1 → XP_054197323.1 intraflagellar transport protein 172 homolog isoform X5