rs1554294443

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4

The NM_001277115.2(DNAH11):​c.13424_13456delCCTACGAGTGCCCTGTGTATAGAACCAAACTGA​(p.Thr4475_Leu4485del) variant causes a disruptive inframe deletion change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

DNAH11
NM_001277115.2 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.95
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_001277115.2.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DNAH11NM_001277115.2 linkuse as main transcriptc.13424_13456delCCTACGAGTGCCCTGTGTATAGAACCAAACTGA p.Thr4475_Leu4485del disruptive_inframe_deletion 82/82 ENST00000409508.8 NP_001264044.1 Q96DT5Q96NT7H9NAJ8H9NAJ7
CDCA7LNM_018719.5 linkuse as main transcriptc.*1165_*1197delAGTTTGGTTCTATACACAGGGCACTCGTAGGTC 3_prime_UTR_variant 10/10 ENST00000406877.8 NP_061189.2 Q96GN5-1A0A024RA51A8K8X5
CDCA7LNM_001127370.3 linkuse as main transcriptc.*1165_*1197delAGTTTGGTTCTATACACAGGGCACTCGTAGGTC 3_prime_UTR_variant 11/11 NP_001120842.1 Q96GN5-4
CDCA7LNM_001127371.3 linkuse as main transcriptc.*1165_*1197delAGTTTGGTTCTATACACAGGGCACTCGTAGGTC 3_prime_UTR_variant 9/9 NP_001120843.1 Q96GN5-5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DNAH11ENST00000409508.8 linkuse as main transcriptc.13424_13456delCCTACGAGTGCCCTGTGTATAGAACCAAACTGA p.Thr4475_Leu4485del disruptive_inframe_deletion 82/825 NM_001277115.2 ENSP00000475939.1 Q96DT5
CDCA7LENST00000406877 linkuse as main transcriptc.*1165_*1197delAGTTTGGTTCTATACACAGGGCACTCGTAGGTC 3_prime_UTR_variant 10/101 NM_018719.5 ENSP00000383986.3 Q96GN5-1

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: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Primary ciliary dyskinesia Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpAug 31, 2021This variant, c.13424_13456del, results in the deletion of 11 amino acid(s) of the DNAH11 protein (p.Thr4475_Leu4485del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with clinical features of DNAH11-related conditions (Invitae). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1554294443; hg19: chr7-21940742; API