7-21543087-CGCGGCTGCTAAGTAGCAGCAGGTGGGAGACTAGGGTCTGCGCTCGCGGCGACCGCGGAGGAGGGTGGGCGCCTGCGGAGGTGTCCTCGCTCACTTCGGGGGGCCCAGAGTCTCGGGTGAGGAGCCAGCCGGCCTCGCGTTCCCTCGGACGGTTGCCCAATGGCAGCCCAGGTGGCAGCCCGGGAGGCGCGAGACTTCAGAGAAGCCCCGACCCTTCGCCTAACCTCGGGGGCCGGCCTGGAGGCAGTGGGCGCTGTGGAGCTCGAGGAGGAGGAGGAGAACGAGGAGGAGGCGGCGGCCAGGAGAGCGCGGAGTTTCGCCCAAGACGCGCGGGTGCGCTTCCTCGGCGGCCGCCTGGCGATGATGCTGGGGTTCACGGAGGAGAAATGGAGCCAGTATTTGGAAAGCGAGGACAACCGGCAGGTTCTTGGGGAGTTTCTGGAAAGCACCAGCCCGGCTTGCCTTGTGTTTAGCTTCGCCGCCTCGGGGCGCCTTGCGGCTTCCC-GGCGCCCCG

Variant summary

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

The NM_001277115.2(DNAH11):c.-159_346delinsGGCGCCCCG variant causes a start lost, 5 prime UTR 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 (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: DNAH11 NM_001277115.2 start_lost, 5_prime_UTR
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 1.14

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]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Start lost variant, no new inframe start found.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 7-21543087-CGCGGCTGCTAAGTAGCAGCAGGTGGGAGACTAGGGTCTGCGCTCGCGGCGACCGCGGAGGAGGGTGGGCGCCTGCGGAGGTGTCCTCGCTCACTTCGGGGGGCCCAGAGTCTCGGGTGAGGAGCCAGCCGGCCTCGCGTTCCCTCGGACGGTTGCCCAATGGCAGCCCAGGTGGCAGCCCGGGAGGCGCGAGACTTCAGAGAAGCCCCGACCCTTCGCCTAACCTCGGGGGCCGGCCTGGAGGCAGTGGGCGCTGTGGAGCTCGAGGAGGAGGAGGAGAACGAGGAGGAGGCGGCGGCCAGGAGAGCGCGGAGTTTCGCCCAAGACGCGCGGGTGCGCTTCCTCGGCGGCCGCCTGGCGATGATGCTGGGGTTCACGGAGGAGAAATGGAGCCAGTATTTGGAAAGCGAGGACAACCGGCAGGTTCTTGGGGAGTTTCTGGAAAGCACCAGCCCGGCTTGCCTTGTGTTTAGCTTCGCCGCCTCGGGGCGCCTTGCGGCTTCCC-GGCGCCCCG is Pathogenic according to our data. Variant chr7-21543087-CGCGGCTGCTAAGTAGCAGCAGGTGGGAGACTAGGGTCTGCGCTCGCGGCGACCGCGGAGGAGGGTGGGCGCCTGCGGAGGTGTCCTCGCTCACTTCGGGGGGCCCAGAGTCTCGGGTGAGGAGCCAGCCGGCCTCGCGTTCCCTCGGACGGTTGCCCAATGGCAGCCCAGGTGGCAGCCCGGGAGGCGCGAGACTTCAGAGAAGCCCCGACCCTTCGCCTAACCTCGGGGGCCGGCCTGGAGGCAGTGGGCGCTGTGGAGCTCGAGGAGGAGGAGGAGAACGAGGAGGAGGCGGCGGCCAGGAGAGCGCGGAGTTTCGCCCAAGACGCGCGGGTGCGCTTCCTCGGCGGCCGCCTGGCGATGATGCTGGGGTTCACGGAGGAGAAATGGAGCCAGTATTTGGAAAGCGAGGACAACCGGCAGGTTCTTGGGGAGTTTCTGGAAAGCACCAGCCCGGCTTGCCTTGTGTTTAGCTTCGCCGCCTCGGGGCGCCTTGCGGCTTCCC-GGCGCCCCG is described in ClinVar as [Pathogenic]. Clinvar id is 2855244.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.-159_346delinsGGCGCCCCG		start_lost, 5_prime_UTR_variant	1/82	ENST00000409508.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH11	ENST00000409508.8	c.-159_346delinsGGCGCCCCG		start_lost, 5_prime_UTR_variant	1/82	5	NM_001277115.2	P1
DNAH11	ENST00000607050.1			non_coding_transcript_exon_variant	1/2	3

Frequencies

GnomAD3 genomes Cov.: 33

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

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

Apr 11, 2023

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with DNAH11-related conditions. This variant results in the deletion of part of exon 1 (c.-159_346delinsGGCGCCCCG) of the DNAH11 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DNAH11 are known to be pathogenic (PMID: 18022865, 20513915, 22184204). -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-21582705;