RSPH1

radial spoke head component 1, the group of Axonemal radial spoke subunits

Basic information

Region (hg38): 21:42472486-42496246

Previous symbols: [ "TSGA2" ]

Links

ENSG00000160188NCBI:89765OMIM:609314HGNC:12371Uniprot:Q8WYR4AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • primary ciliary dyskinesia 24 (Strong), mode of inheritance: AR
  • primary ciliary dyskinesia 24 (Strong), mode of inheritance: AR
  • primary ciliary dyskinesia (Supportive), mode of inheritance: AD
  • primary ciliary dyskinesia 24 (Moderate), mode of inheritance: AR
  • primary ciliary dyskinesia 24 (Definitive), mode of inheritance: AR
  • primary ciliary dyskinesia 24 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Ciliary dyskinesia, primary, 24ARAllergy/Immunology/Infectious; Audiologic/Otolaryngologic; PulmonaryPulmonary and audiologic surveillance may be beneficial to assess respiratory and hearing function and institute early management measures; In order to facilitate mucus clearance, aggressive interventions (eg, chest percussion and oscillatory vest), as well as vaccinations and early and aggressive treatment of respiratory infections may be beneficialAllergy/Immunology/Infectious; Audiologic/Otolaryngologic; Genitourinary; Pulmonary20301301; 23993197; 24518672

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RSPH1 gene.

  • Primary_ciliary_dyskinesia (204 variants)
  • Inborn_genetic_diseases (48 variants)
  • not_provided (34 variants)
  • Primary_ciliary_dyskinesia_24 (22 variants)
  • RSPH1-related_disorder (13 variants)
  • Kartagener_syndrome (3 variants)
  • not_specified (2 variants)
  • Respiratory_ciliopathies_including_non-CF_bronchiectasis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RSPH1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000080860.4. 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
3
clinvar
57
clinvar
4
clinvar
64
missense
1
clinvar
1
clinvar
85
clinvar
11
clinvar
98
nonsense
5
clinvar
5
clinvar
1
clinvar
11
start loss
1
1
frameshift
8
clinvar
1
clinvar
9
splice donor/acceptor (+/-2bp)
3
clinvar
2
clinvar
1
clinvar
6
Total 18 9 90 68 4

Highest pathogenic variant AF is 0.000704207

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RSPH1protein_codingprotein_codingENST00000291536 923869
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.000002050.89812564101071257480.000426
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1381861910.9720.00001142022
Missense in Polyphen6070.4660.85148759
Synonymous-0.2477774.31.040.00000492552
Loss of Function1.611219.70.6089.03e-7230

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001060.00106
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.00004620.0000462
European (Non-Finnish)0.0005360.000519
Middle Eastern0.00005440.0000544
South Asian0.0002610.000261
Other0.0009780.000978

dbNSFP

Source: dbNSFP

Function
FUNCTION: May play an important role in male meiosis (By similarity). It is necessary for proper building of the axonemal central pair and radial spokes. {ECO:0000250, ECO:0000269|PubMed:23993197}.;

Recessive Scores

pRec
0.0951

Intolerance Scores

loftool
0.788
rvis_EVS
0.49
rvis_percentile_EVS
79.52

Haploinsufficiency Scores

pHI
0.0512
hipred
N
hipred_score
0.205
ghis
0.426

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.112

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rsph1
Phenotype
reproductive system phenotype; cellular phenotype; growth/size/body region phenotype;

Gene ontology

Biological process
spermatid development;axoneme assembly;meiotic cell cycle
Cellular component
condensed nuclear chromosome;outer dense fiber;nucleus;cytosol;motile cilium;meiotic spindle
Molecular function
protein binding