RSPH1

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

Basic information

Region (hg38): 21:42472486-42496246

Previous symbols: [ "TSGA2" ]

Links

ENSG00000160188

∙ NCBI:89765 ∙ OMIM:609314 ∙ HGNC:12371 ∙ Uniprot:Q8WYR4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ciliary dyskinesia, primary, 24	AR	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Pulmonary	Pulmonary 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 beneficial	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Genitourinary; Pulmonary	20301301; 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
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

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RSPH1	protein_coding	protein_coding	ENST00000291536	9	23869

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000205	0.898	125641	0	107	125748	0.000426

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.138	186	191	0.972	0.0000114	2022
Missense in Polyphen		60	70.466	0.85148		759
Synonymous	-0.247	77	74.3	1.04	0.00000492	552
Loss of Function	1.61	12	19.7	0.608	9.03e-7	230

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00106	0.00106
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000536	0.000519
Middle Eastern	0.0000544	0.0000544
South Asian	0.000261	0.000261
Other	0.000978	0.000978

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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