rs1554248887

Variant names:

• chr7-727208-ACCTGGACGAC-A
• rs1554248887
• NM_017802.4:c.489_498delCCTGGACGAC

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_Moderate PM2 PP5_Moderate

The NM_001164760.2(PRKAR1B):​c.-31_-23+1delGTCGTCCAGG variant causes a splice donor, 5 prime UTR, intron change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: PRKAR1B NM_001164760.2 splice_donor, 5_prime_UTR, intron
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 6.58

Genes affected

DNAAF5 (HGNC:26013): (dynein axonemal assembly factor 5) The protein encoded by this gene is essential for the preassembly or stability of axonemal dynein arms, and is found only in organisms with motile cilia and flagella. Mutations in this gene are associated with primary ciliary dyskinesia-18, a disorder characterized by abnormalities of motile cilia. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Feb 2013]

PRKAR1B (HGNC:9390): (protein kinase cAMP-dependent type I regulatory subunit beta) The protein encoded by this gene is a regulatory subunit of cyclic AMP-dependent protein kinase A (PKA), which is involved in the signaling pathway of the second messenger cAMP. Two regulatory and two catalytic subunits form the PKA holoenzyme, disbands after cAMP binding. The holoenzyme is involved in many cellular events, including ion transport, metabolism, and transcription. Several transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Aug 2015]

ACMG classification

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.06282722 fraction of the gene.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 7-727208-ACCTGGACGAC-A is Pathogenic according to our data. Variant chr7-727208-ACCTGGACGAC-A is described in ClinVar as [Pathogenic]. Clinvar id is 454865.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAAF5	NM_017802.4	c.489_498delCCTGGACGAC	p.His163GlnfsTer43	frameshift_variant	Exon 1 of 13	ENST00000297440.11	NP_060272.3
PRKAR1B	NM_001164760.2	c.-31_-23+1delGTCGTCCAGG		splice_region_variant	Exon 1 of 11	ENST00000537384.6	NP_001158232.1
PRKAR1B	NM_001164760.2	c.-31_-23+1delGTCGTCCAGG		splice_donor_variant, 5_prime_UTR_variant, intron_variant	Exon 1 of 11	ENST00000537384.6	NP_001158232.1
PRKAR1B	NM_001164760.2	c.-31_-23+1delGTCGTCCAGG		non_coding_transcript_variant		ENST00000537384.6	NP_001158232.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAAF5	ENST00000297440.11	c.489_498delCCTGGACGAC	p.His163GlnfsTer43	frameshift_variant	Exon 1 of 13	1	NM_017802.4	ENSP00000297440.6
PRKAR1B	ENST00000537384.6	c.-31_-23+1delGTCGTCCAGG		splice_region_variant	Exon 1 of 11	5	NM_001164760.2	ENSP00000440449.1
PRKAR1B	ENST00000537384.6	c.-31_-23+1delGTCGTCCAGG		splice_donor_variant, 5_prime_UTR_variant, intron_variant	Exon 1 of 11	5	NM_001164760.2	ENSP00000440449.1
PRKAR1B	ENST00000537384.6	c.-31_-23+1delGTCGTCCAGG		non_coding_transcript_variant		5	NM_001164760.2	ENSP00000440449.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Primary ciliary dyskinesia Pathogenic:1

Jul 05, 2022

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. This sequence change creates a premature translational stop signal (p.His163Glnfs*43) in the DNAAF5 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DNAAF5 are known to be pathogenic (PMID: 24307375, 25232951). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with DNAAF5-related conditions. ClinVar contains an entry for this variant (Variation ID: 454865). -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1554248887; hg19: chr7-766845;