RPGRIP1L RPGRIP1 like [Homo sapiens (human)] - Gene

Summary

Official Symbol: RPGRIP1Lprovided by HGNC
Official Full Name: RPGRIP1 likeprovided by HGNC
Primary source: HGNC:HGNC:29168
See related: Ensembl:ENSG00000103494 MIM:610937; AllianceGenome:HGNC:29168
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: FTM; MKS5; CORS3; JBTS7; NPHP8; COACH3; PPP1R134
Summary: The protein encoded by this gene can localize to the basal body-centrosome complex or to primary cilia and centrosomes in ciliated cells. The encoded protein has been found to interact with nephrocystin-4. Defects in this gene are a cause of Joubert syndrome type 7 (JBTS7) and Meckel syndrome type 5 (MKS5). [provided by RefSeq, Jun 2016]
Expression: Broad expression in testis (RPKM 3.8), brain (RPKM 1.3) and 19 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16q12.2

Exon count:: 36

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (53598153..53703859, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (59395985..59501692, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (53632065..53737771, complement)

Chromosome 16 - NC_000016.10 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Identification of Pathogenic Variants in RPGRIP1L with Meckel Syndrome and Preimplantation Genetic Testing in a Chinese Family.
Title: Identification of Pathogenic Variants in RPGRIP1L with Meckel Syndrome and Preimplantation Genetic Testing in a Chinese Family.
Rpgrip1l controls ciliary gating by ensuring the proper amount of Cep290 at the vertebrate transition zone.
Title: Rpgrip1l controls ciliary gating by ensuring the proper amount of Cep290 at the vertebrate transition zone.
The Major Ciliary Isoforms of RPGR Build Different Interaction Complexes with INPP5E and RPGRIP1L.
Title: The Major Ciliary Isoforms of RPGR Build Different Interaction Complexes with INPP5E and RPGRIP1L.
it might be reasonable to consider RPGRIP1L as an important gene whose variations could be associated with obesity risk factors.
Title: A novel association of rs13334070 in the RPGRIP1L gene with adiposity factors discovered by joint linkage and linkage disequilibrium analysis in Iranian pedigrees: Tehran Cardiometabolic Genetic Study (TCGS).
T allele in RPGRIP1L gene might increase the risk of vitiligo in a Chinese Han population.
Title: Rs3213758 in the RPGRIP1L Gene Associated with Susceptibility to Segmental Vitiligo in a Chinese Han Population.
Biotinylation assays on cell surface proteins not only reinforced the role of RPGRIP1L in desmoglein endocytosis, but also suggested that RPGRIP1L may be more broadly involved in endocytosis. Thus, data obtained from this study advanced our understanding of the biological functions of RPGRIP1L by identifying its role in the cellular endocytic pathway.
Title: RPGRIP1L is required for stabilizing epidermal keratinocyte adhesion through regulating desmoglein endocytosis.
Loss of Rpgrip1l expression is associated with Ciliopathy.
Title: Cell type-specific regulation of ciliary transition zone assembly in vertebrates.
we didn't found the significant association between RPGRIP1L and BMI in Chinese women
Title: Association of fat mass and obesity-associated and retinitis pigmentosa guanosine triphosphatase (GTPase) regulator-interacting protein-1 like polymorphisms with body mass index in Chinese women.
our studies revealed RPGRIP1L as a novel MyoVa-binding protein - the first to be demonstrated to interact with MyoVa at the centrosome - and uncover an unprecedented link between MyoVa and ciliogenesis, providing new perspectives for studies aiming to better understand why defects in MyoVa cause neurological disorders in Griscelli syndrome patients.
Title: The molecular motor Myosin Va interacts with the cilia-centrosomal protein RPGRIP1L.
Importantly, one Japanese and one Omani families carried compound biallelic mutations in two distinct genes (TMEM67/RPGRIP1L and TMEM138/BBS1, respectively).
Title: Molecular genetic analysis of 30 families with Joubert syndrome.

Submit: New GeneRIF Correction See all GeneRIFs (30)

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
COACH syndrome 3 MedGen: C5436841 OMIM: 619113 GeneReviews: Not available	not available
Familial aplasia of the vermis MedGen: C0431399 GeneReviews: Joubert Syndrome	not available
Joubert syndrome 7 MedGen: C1969053 OMIM: 611560 GeneReviews: Joubert Syndrome	not available
Meckel syndrome, type 5 MedGen: C1969052 OMIM: 611561 GeneReviews: Not available	not available
Nephronophthisis 8 MedGen: CN119610 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Propensity score-based nonparametric test revealing genetic variants underlying bipolar disorder. EBI GWAS Catalog EBI GWAS CatalogPubMed
Three new single nucleotide polymorphisms identified by a genome-wide association study in Korean patients with vitiligo. 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

D16S3137 (e-PCR)
- UniSTS:46611

RH123056 (e-PCR)
- UniSTS:135449

SHGC-60833 (e-PCR)
- UniSTS:14938

SHGC-151097 (e-PCR)
- UniSTS:173248

WI-11251 (e-PCR)
- UniSTS:76537

D16S415 (e-PCR)
- UniSTS:30459

SHGC-56694 (e-PCR)
- UniSTS:62203

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables thromboxane A2 receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables thromboxane A2 receptor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cerebellum development	IEA Inferred from Electronic Annotation more info
involved_in cochlea development	IEA Inferred from Electronic Annotation more info
involved_in corpus callosum development	IEA Inferred from Electronic Annotation more info
involved_in determination of left/right symmetry	IEA Inferred from Electronic Annotation more info
involved_in embryonic forelimb morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in embryonic hindlimb morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in establishment of planar polarity	IEA Inferred from Electronic Annotation more info
involved_in establishment or maintenance of cell polarity	IEA Inferred from Electronic Annotation more info
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
involved_in kidney development	IEA Inferred from Electronic Annotation more info
involved_in lateral ventricle development	IEA Inferred from Electronic Annotation more info
involved_in liver development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of G protein-coupled receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in neural tube patterning	IEA Inferred from Electronic Annotation more info
involved_in non-motile cilium assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in nose development	IEA Inferred from Electronic Annotation more info
involved_in olfactory bulb development	IEA Inferred from Electronic Annotation more info
involved_in pericardium development	IEA Inferred from Electronic Annotation more info
involved_in regulation of smoothened signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in retinal rod cell development	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in axonemal microtubule	IEA Inferred from Electronic Annotation more info
located_in axoneme	IDA Inferred from Direct Assay more info	PubMed
located_in bicellular tight junction	IEA Inferred from Electronic Annotation more info
located_in cell-cell junction	IDA Inferred from Direct Assay more info	PubMed
located_in centrosome	IDA Inferred from Direct Assay more info	PubMed
located_in ciliary basal body	IDA Inferred from Direct Assay more info	PubMed
located_in ciliary rootlet	IEA Inferred from Electronic Annotation more info
located_in ciliary transition zone	IDA Inferred from Direct Assay more info	PubMed
located_in cilium	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in photoreceptor connecting cilium	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: protein fantom

Names: RPGR-interacting protein 1-like protein; fantom homolog; nephrocystin-8; protein phosphatase 1, regulatory subunit 134

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_008991.2 RefSeqGene

Range

5001..110707

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_696

mRNA and Protein(s)

NM_001127897.4 → NP_001121369.1 protein fantom isoform b

See identical proteins and their annotated locations for NP_001121369.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks two alternate in-frame exons compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.

Source sequence(s)

AB023222, AC007497, CR749645, DC423209

Consensus CDS

CCDS45486.1

UniProtKB/TrEMBL

B7ZKJ9

Related

ENSP00000262135.4, ENST00000262135.9

Conserved Domains (4) summary

cd00030
Location:792 → 891

C2; C2 domain

pfam06818
Location:244 → 445

Fez1; Fez1

pfam11618
Location:598 → 737

C2-C2_1; First C2 domain of RPGR-interacting protein 1

cl23720
Location:214 → 350

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
NM_001308334.3 → NP_001295263.1 protein fantom isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an in-frame exon in the central coding region compared to variant 1. The encoded isoform (c) is shorter than isoform a.

Source sequence(s)

AC007497, BC136433, BX340768, R45454

Consensus CDS

CCDS76868.1

UniProtKB/TrEMBL

A0A087WX34, B7ZKJ9

Related

ENSP00000480698.1, ENST00000621565.5

Conserved Domains (4) summary

cd00030
Location:792 → 891

C2; C2 domain

pfam06818
Location:244 → 445

Fez1; Fez1

pfam11618
Location:598 → 737

C2-C2_1; First C2 domain of RPGR-interacting protein 1

cl23720
Location:214 → 350

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
NM_001328422.2 → NP_001315351.1 protein fantom isoform d

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks several 3' exons, and uses an alternate 3' terminal exon, compared to variant 1. The encoded isoform (d) has a shorter and distinct C-terminus compared to isoform a.

Source sequence(s)

AC007909, BX340768, CA313857, EF565106

Consensus CDS

CCDS86527.1

UniProtKB/TrEMBL

H3BPS4

Related

ENSP00000455451.3, ENST00000568653.7
NM_001328423.2 → NP_001315352.1 protein fantom isoform e

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks several 3' exons, and has a 3' end that extends into an intron compared to variant 1. The encoded isoform (e) has a shorter and distinct C-terminus compared to isoform a.

Source sequence(s)

AC007909, BX340768, CD674885

Consensus CDS

CCDS86526.1

UniProtKB/TrEMBL

I3L1B5

Related

ENSP00000458705.1, ENST00000566096.5
NM_001330538.2 → NP_001317467.1 protein fantom isoform f

Status: REVIEWED

Description

Transcript Variant: This variant (6) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (f) is shorter than isoform 1.

Source sequence(s)

AC007497, AC084795, AK307929, BX340768, R45454

Consensus CDS

CCDS81980.1

UniProtKB/TrEMBL

B7ZKJ9, H3BV03

Related

ENSP00000457889.1, ENST00000563746.5

Conserved Domains (5) summary

cd00030
Location:792 → 891

C2; C2 domain

pfam06818
Location:244 → 445

Fez1; Fez1

pfam10482
Location:338 → 459

CtIP_N; Tumour-suppressor protein CtIP N-terminal domain

pfam11618
Location:598 → 737

C2-C2_1; First C2 domain of RPGR-interacting protein 1

cl23720
Location:214 → 350

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
NM_015272.5 → NP_056087.2 protein fantom isoform a

See identical proteins and their annotated locations for NP_056087.2

Status: REVIEWED

Description

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

Source sequence(s)

AC007497, AC007909, CR749645

Consensus CDS

CCDS32447.1

UniProtKB/Swiss-Prot

A0PJ88, Q68CZ1, Q9Y2K8

UniProtKB/TrEMBL

B7ZKJ9

Related

ENSP00000493946.1, ENST00000647211.2

Conserved Domains (5) summary

cd00030
Location:792 → 891

C2; C2 domain

pfam06818
Location:244 → 445

Fez1; Fez1

pfam10482
Location:338 → 459

CtIP_N; Tumour-suppressor protein CtIP N-terminal domain

pfam11618
Location:598 → 737

C2-C2_1; First C2 domain of RPGR-interacting protein 1

cl23720
Location:214 → 350

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

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_000016.10 Reference GRCh38.p14 Primary Assembly

Range

53598153..53703859 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017023095.3 → XP_016878584.1 protein fantom isoform X5

UniProtKB/TrEMBL

B7ZKJ9
XM_005255868.3 → XP_005255925.1 protein fantom isoform X4

UniProtKB/TrEMBL

B7ZKJ9

Conserved Domains (4) summary

cd00030
Location:796 → 895

C2; C2 domain

pfam06818
Location:244 → 449

Fez1; Fez1

pfam11618
Location:602 → 741

C2-C2_1; First C2 domain of RPGR-interacting protein 1

cl23720
Location:214 → 350

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
XM_047433872.1 → XP_047289828.1 protein fantom isoform X6

UniProtKB/TrEMBL

B7ZKJ9
XM_047433871.1 → XP_047289827.1 protein fantom isoform X3

UniProtKB/TrEMBL

B7ZKJ9, H3BV03
XM_047433870.1 → XP_047289826.1 protein fantom isoform X2

UniProtKB/Swiss-Prot

A0PJ88, Q68CZ1, Q9Y2K8

UniProtKB/TrEMBL

B7ZKJ9
XM_047433869.1 → XP_047289825.1 protein fantom isoform X1

UniProtKB/TrEMBL

B7ZKJ9
XM_017023099.2 → XP_016878588.1 protein fantom isoform X20
XM_017023098.2 → XP_016878587.1 protein fantom isoform X20
XM_047433878.1 → XP_047289834.1 protein fantom isoform X15

UniProtKB/TrEMBL

A0A7P0TB06
XM_047433873.1 → XP_047289829.1 protein fantom isoform X7

UniProtKB/TrEMBL

A0A7P0TB06
XM_047433874.1 → XP_047289830.1 protein fantom isoform X9

UniProtKB/TrEMBL

A0A7P0TB06
XM_047433877.1 → XP_047289833.1 protein fantom isoform X14

UniProtKB/TrEMBL

A0A7P0TB06
XM_047433875.1 → XP_047289831.1 protein fantom isoform X11

UniProtKB/TrEMBL

A0A7P0TB06
XM_011522971.4 → XP_011521273.1 protein fantom isoform X10

UniProtKB/TrEMBL

A0A7P0TB06

Conserved Domains (3) summary

cd00030
Location:796 → 895

C2; C2 domain

pfam06818
Location:244 → 449

Fez1; Fez1

pfam11618
Location:602 → 741

C2-C2_1; First C2 domain of RPGR-interacting protein 1
XM_047433879.1 → XP_047289835.1 protein fantom isoform X16

UniProtKB/TrEMBL

A0A7P0TB06
XM_011522970.3 → XP_011521272.1 protein fantom isoform X8

UniProtKB/TrEMBL

A0A7P0TB06

Conserved Domains (4) summary

cd00030
Location:796 → 895

C2; C2 domain

pfam06818
Location:244 → 449

Fez1; Fez1

pfam11618
Location:602 → 741

C2-C2_1; First C2 domain of RPGR-interacting protein 1

cl23720
Location:214 → 350

RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
XM_047433881.1 → XP_047289837.1 protein fantom isoform X18

UniProtKB/TrEMBL

A0A7P0TB06
XM_047433876.1 → XP_047289832.1 protein fantom isoform X13

UniProtKB/TrEMBL

A0A7P0TB06
XM_047433880.1 → XP_047289836.1 protein fantom isoform X17

UniProtKB/TrEMBL

A0A7P0TB06
XM_011522973.4 → XP_011521275.1 protein fantom isoform X12

UniProtKB/TrEMBL

A0A7P0TB06

Conserved Domains (3) summary

cd00030
Location:796 → 895

C2; C2 domain

pfam06818
Location:244 → 449

Fez1; Fez1

pfam11618
Location:602 → 741

C2-C2_1; First C2 domain of RPGR-interacting protein 1
XM_017023097.3 → XP_016878586.1 protein fantom isoform X19
XM_017023100.3 → XP_016878589.1 protein fantom isoform X21