GeneBe

IMPG1

interphotoreceptor matrix proteoglycan 1

Basic information

Region (hg38): 6:75921114-76072678

Previous symbols: [ "SPACR" ]

Links

ENSG00000112706 ∙ NCBI:3617 ∙ OMIM:602870 ∙ HGNC:6055 ∙ Uniprot:Q17R60 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • retinitis pigmentosa (Moderate), mode of inheritance: AR
  • retinitis pigmentosa (Moderate), mode of inheritance: AD
  • vitelliform macular dystrophy 4 (Moderate), mode of inheritance: AD
  • adult-onset foveomacular vitelliform dystrophy (Supportive), mode of inheritance: AD
  • vitelliform macular dystrophy 4 (Definitive), mode of inheritance: AD
  • vitelliform macular dystrophy 4 (Strong), mode of inheritance: AD
  • inherited retinal dystrophy (Definitive), mode of inheritance: AD
  • vitelliform macular dystrophy 4 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Macular dystrophy, vitelliform, 4; Retinitis pigmentosa 91; Retinitis pigmentosa 56AD/ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingOphthalmologic23993198; 25085631; 30589393; 32817297

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IMPG1 gene.

  • not_provided (642 variants)
  • not_specified (113 variants)
  • Retinal_dystrophy (67 variants)
  • IMPG1-related_disorder (19 variants)
  • Vitelliform_macular_dystrophy_4 (18 variants)
  • Benign_concentric_annular_macular_dystrophy (9 variants)
  • Retinitis_pigmentosa (7 variants)
  • Macular_dystrophy (1 variants)
  • Incidental_Discovery (1 variants)
  • Cone-rod_dystrophy (1 variants)
  • Vitelliform_macular_dystrophy_1 (1 variants)
  • Vitelliform_macular_dystrophy_2 (1 variants)
  • Isolated_macular_dystrophy (1 variants)
  • Vitelliform_macular_dystrophy_5 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IMPG1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001563.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
9
clinvar
120
clinvar
5
clinvar
 134
missense
3
clinvar
5
clinvar
366
clinvar
26
clinvar
11
clinvar
 411
nonsense
13
clinvar
5
clinvar
4
clinvar
 22
start loss
2
 2
frameshift
25
clinvar
6
clinvar
5
clinvar
 36
splice donor/acceptor (+/-2bp)
4
clinvar
12
clinvar
3
clinvar
 19
Total 45 28 389 146 16

Highest pathogenic variant AF is 0.000115345116

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
IMPG1protein_codingprotein_codingENST00000369950 17151564
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.37e-290.00003391256700781257480.000310
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.9374764221.130.00002115242
Missense in Polyphen10697.6981.0851337
Synonymous0.08781541550.9910.000008631509
Loss of Function-0.2954341.01.050.00000225471

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0007540.000631
Ashkenazi Jewish0.00009970.0000992
East Asian0.0004350.000435
Finnish0.000.00
European (Non-Finnish)0.0003560.000352
Middle Eastern0.0004350.000435
South Asian0.0004390.000425
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: May interact with hyaluronan which may serve to form a basic macromolecular scaffold comprising the insoluble interphotoreceptor matrix. {ECO:0000269|PubMed:9813076}.;
Disease
DISEASE: Macular dystrophy, vitelliform, 4 (VMD4) [MIM:616151]: A form of macular dystrophy, a retinal disease in which various forms of deposits, pigmentary changes, and atrophic lesions are observed in the macula lutea. Vitelliform macular dystrophies are characterized by yellow, lipofuscin-containing deposits, usually localized at the center of the macula. VMD4 features include late- onset moderate visual impairment, small satellite drusen-like lesions in the foveal area, and preservation of retinal pigment epithelium reflectivity. {ECO:0000269|PubMed:23993198}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.0918

Intolerance Scores

loftool
0.964
rvis_EVS
0.69
rvis_percentile_EVS
85.29

Haploinsufficiency Scores

pHI
0.269
hipred
N
hipred_score
0.112
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.0100

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Impg1
Phenotype

Gene ontology

Biological process
visual perception
Cellular component
extracellular matrix
Molecular function
extracellular matrix structural constituent