RSPH6A

radial spoke head 6 homolog A, the group of Axonemal radial spoke subunits

Basic information

Region (hg38): 19:45795713-45815308

Previous symbols: [ "RSHL1" ]

Links

ENSG00000104941 ∙ NCBI:81492 ∙ OMIM:607548 ∙ HGNC:14241 ∙ Uniprot:Q9H0K4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RSPH6A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RSPH6A gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			76	1		77
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	76	2	0

Variants in RSPH6A

This is a list of pathogenic ClinVar variants found in the RSPH6A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-45795879-G-T		not specified	Uncertain significance (May 26, 2024)
19-45795886-C-G		not specified	Uncertain significance (Aug 21, 2024)
19-45795920-C-T			Likely benign (May 08, 2018)
19-45795938-T-A		not specified	Uncertain significance (Apr 13, 2022)
19-45796030-T-G		not specified	Uncertain significance (Jan 23, 2024)
19-45796060-C-T		not specified	Uncertain significance (Jul 27, 2021)
19-45796094-G-C		not specified	Uncertain significance (Jan 24, 2024)
19-45800467-G-A		not specified	Uncertain significance (Oct 07, 2022)
19-45800468-C-A		not specified	Uncertain significance (Dec 12, 2023)
19-45800533-C-T		not specified	Uncertain significance (May 17, 2023)
19-45802140-G-A		not specified	Uncertain significance (Nov 10, 2023)
19-45802149-G-C		not specified	Uncertain significance (Aug 12, 2024)
19-45802149-G-T		not specified	Uncertain significance (Feb 22, 2023)
19-45802224-T-C		not specified	Uncertain significance (Jun 22, 2023)
19-45802249-C-T		not specified	Uncertain significance (Dec 10, 2024)
19-45804307-T-G		not specified	Uncertain significance (Nov 10, 2022)
19-45804310-A-G		not specified	Uncertain significance (Oct 10, 2023)
19-45804324-C-G		not specified	Uncertain significance (Mar 24, 2023)
19-45804326-C-T		not specified	Uncertain significance (May 15, 2023)
19-45804361-G-C		not specified	Uncertain significance (Jul 13, 2021)
19-45804367-C-T		not specified	Uncertain significance (Nov 30, 2022)
19-45804376-T-A		not specified	Uncertain significance (Aug 03, 2022)
19-45804391-T-A		not specified	Uncertain significance (Aug 23, 2021)
19-45804434-C-T		not specified	Uncertain significance (Oct 29, 2024)
19-45804473-C-A		not specified	Uncertain significance (Sep 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RSPH6A	protein_coding	protein_coding	ENST00000221538	6	19610

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.34e-10	0.876	125647	1	100	125748	0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.429	476	450	1.06	0.0000284	4684
Missense in Polyphen		119	122.75	0.96943		1232
Synonymous	0.288	202	207	0.975	0.0000153	1394
Loss of Function	1.80	20	30.8	0.650	0.00000150	321

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000934	0.000933
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.000435	0.000435
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000541	0.000528
Middle Eastern	0.000435	0.000435
South Asian	0.0000980	0.0000980
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.820
• rvis_EVS: -1.06
• rvis_percentile_EVS: 7.58

Haploinsufficiency Scores

• pHI: 0.0719
• hipred: N
• hipred_score: 0.146
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rsph6a
• Phenotype: cellular phenotype; reproductive system phenotype