rs1555875358

Variant names:

• chr21-42477152-CCCACAGCCCGGGGATGCCCCACACCCTCTGACCCCTCCACCCCACAGCCCGGGGATGCCCCACACCCTCTGTCCCACAGCCCGGGGGTGCCCCACACCCTCTGCCCCCTCCACCCCACAGCCCGGGGGTGCCCCACACT-C
• rs1555875358
• NM_080860.4:c.727_727+138del

Variant summary

Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PVS1 PP5_Moderate

The NM_080860.4(RSPH1):​c.727_727+138del​(p.Ser243fs) variant causes a frameshift, splice donor, splice region, intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 20)
• Consequence: RSPH1 NM_080860.4 frameshift, splice_donor, splice_region, intron
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 1.02
• Publications: 0 publications found

Genes affected

RSPH1 (HGNC:12371): (radial spoke head component 1) This gene encodes a male meiotic metaphase chromosome-associated acidic protein. This gene is expressed in tissues with motile cilia or flagella, including the trachea, lungs, airway brushings, and testes. Mutations in this gene result in primary ciliary dyskinesia-24. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2014]

RSPH1 Gene-Disease associations (from GenCC):

• primary ciliary dyskinesia 24

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: ClinGen, Ambry Genetics, PanelApp Australia, G2P, Labcorp Genetics (formerly Invitae)
• primary ciliary dyskinesia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 10 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PP5: Variant 21-42477152-CCCACAGCCCGGGGATGCCCCACACCCTCTGACCCCTCCACCCCACAGCCCGGGGATGCCCCACACCCTCTGTCCCACAGCCCGGGGGTGCCCCACACCCTCTGCCCCCTCCACCCCACAGCCCGGGGGTGCCCCACACT-C is Pathogenic according to our data. Variant chr21-42477152-CCCACAGCCCGGGGATGCCCCACACCCTCTGACCCCTCCACCCCACAGCCCGGGGATGCCCCACACCCTCTGTCCCACAGCCCGGGGGTGCCCCACACCCTCTGCCCCCTCCACCCCACAGCCCGGGGGTGCCCCACACT-C is described in ClinVar as Pathogenic. ClinVar VariationId is 454950.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080860.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RSPH1	NM_080860.4	MANE Select	c.727_727+138del	p.Ser243fs	frameshift splice_donor splice_region intron	Exon 7 of 9	NP_543136.1
	RSPH1	NM_001286506.2		c.613_613+138del	p.Ser205fs	frameshift splice_donor splice_region intron	Exon 6 of 8	NP_001273435.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RSPH1	ENST00000291536.8	TSL:1 MANE Select	c.727_727+138del	p.Ser243fs	frameshift splice_donor splice_region intron	Exon 7 of 9	ENSP00000291536.3
	RSPH1	ENST00000398352.3	TSL:5	c.613_613+138del	p.Ser205fs	frameshift splice_donor splice_region intron	Exon 6 of 8	ENSP00000381395.3
	RSPH1	ENST00000493019.1	TSL:2	n.2345_2345+138del		splice_donor splice_region intron non_coding_transcript_exon	Exon 6 of 8

Frequencies

GnomAD3 genomes Cov.: 20

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 20

ClinVar

ClinVar submissions as Germline

Significance: Pathogenic

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
1	-	-	Primary ciliary dyskinesia (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.0
Mutation Taster		=25/175	disease causing (ClinVar)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1555875358; hg19: chr21-43897262;