7-21901021-A-ACCCAAGCAGGAACCATTGTTGAAGCCCGTCTCAAGGAGCTGGCATGCCCTATGCCGGTCATCTTTGCAAAAGCCACCCCCGTGGACAGACAAGAAAC

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_001277115.2(DNAH11):c.13320_13416dup(p.Lys4473ProfsTer7) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. T4440T) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: DNAH11 NM_001277115.2 frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: -0.590

Genes affected

DNAH11 (HGNC:2942): (dynein axonemal heavy chain 11) This gene encodes a ciliary outer dynein arm protein and is a member of the dynein heavy chain family. It is a microtubule-dependent motor ATPase and has been reported to be involved in the movement of respiratory cilia. Mutations in this gene have been implicated in causing Kartagener Syndrome (a combination of situs inversus totalis and Primary Ciliary Dyskinesia (PCD), also called Immotile Cilia Syndrome 1 (ICS1)) and male sterility. [provided by RefSeq, Mar 2013]

CDCA7L (HGNC:30777): (cell division cycle associated 7 like) Acts upstream of or within positive regulation of cell population proliferation. Located in cytosol; fibrillar center; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 24 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 7-21901021-A-ACCCAAGCAGGAACCATTGTTGAAGCCCGTCTCAAGGAGCTGGCATGCCCTATGCCGGTCATCTTTGCAAAAGCCACCCCCGTGGACAGACAAGAAAC is Pathogenic according to our data. Variant chr7-21901021-A-ACCCAAGCAGGAACCATTGTTGAAGCCCGTCTCAAGGAGCTGGCATGCCCTATGCCGGTCATCTTTGCAAAAGCCACCCCCGTGGACAGACAAGAAAC is described in ClinVar as [Pathogenic]. Clinvar id is 936022.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH11	NM_001277115.2	c.13320_13416dup	p.Lys4473ProfsTer7	frameshift_variant	82/82	ENST00000409508.8
CDCA7L	NM_018719.5	c.*1300_*1301insGTTTCTTGTCTGTCCACGGGGGTGGCTTTTGCAAAGATGACCGGCATAGGGCATGCCAGCTCCTTGAGACGGGCTTCAACAATGGTTCCTGCTTGGG		3_prime_UTR_variant	10/10	ENST00000406877.8
CDCA7L	NM_001127370.3	c.*1300_*1301insGTTTCTTGTCTGTCCACGGGGGTGGCTTTTGCAAAGATGACCGGCATAGGGCATGCCAGCTCCTTGAGACGGGCTTCAACAATGGTTCCTGCTTGGG		3_prime_UTR_variant	11/11
CDCA7L	NM_001127371.3	c.*1300_*1301insGTTTCTTGTCTGTCCACGGGGGTGGCTTTTGCAAAGATGACCGGCATAGGGCATGCCAGCTCCTTGAGACGGGCTTCAACAATGGTTCCTGCTTGGG		3_prime_UTR_variant	9/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH11	ENST00000409508.8	c.13320_13416dup	p.Lys4473ProfsTer7	frameshift_variant	82/82	5	NM_001277115.2	P1
CDCA7L	ENST00000406877.8	c.*1300_*1301insGTTTCTTGTCTGTCCACGGGGGTGGCTTTTGCAAAGATGACCGGCATAGGGCATGCCAGCTCCTTGAGACGGGCTTCAACAATGGTTCCTGCTTGGG		3_prime_UTR_variant	10/10	1	NM_018719.5	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Primary ciliary dyskinesia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Sep 10, 2021

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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: rs1784790883; hg19: chr7-21940639;