rs189432084

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The NM_001277115.2(DNAH11):​c.5132A>C​(p.Gln1711Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,448,072 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q1711R) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 31)
Exomes š‘“: 0.0000014 ( 0 hom. )

Consequence

DNAH11
NM_001277115.2 missense

Scores

1
6
10

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.471
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.794

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DNAH11NM_001277115.2 linkc.5132A>C p.Gln1711Pro missense_variant Exon 30 of 82 ENST00000409508.8 NP_001264044.1 Q96DT5Q96NT7H9NAJ8H9NAJ7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DNAH11ENST00000409508.8 linkc.5132A>C p.Gln1711Pro missense_variant Exon 30 of 82 5 NM_001277115.2 ENSP00000475939.1 Q96DT5

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
AF:
0.00000138
AC:
2
AN:
1448072
Hom.:
0
Cov.:
31
AF XY:
0.00000139
AC XY:
1
AN XY:
718790
show subpopulations
Gnomad4 AFR exome
AF:
0.0000301
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.05e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.35
BayesDel_addAF
Benign
0.0088
T
BayesDel_noAF
Benign
-0.23
CADD
Benign
17
DANN
Uncertain
0.98
DEOGEN2
Uncertain
0.74
.;.;D
Eigen
Benign
-0.61
Eigen_PC
Benign
-0.61
FATHMM_MKL
Benign
0.33
N
LIST_S2
Benign
0.85
D;D;D
M_CAP
Benign
0.032
D
MetaRNN
Pathogenic
0.79
D;D;D
MetaSVM
Benign
-0.92
T
PrimateAI
Benign
0.31
T
PROVEAN
Uncertain
-2.5
.;D;.
REVEL
Uncertain
0.30
Sift
Uncertain
0.0050
.;D;.
Vest4
0.66
MutPred
0.72
Gain of phosphorylation at T1718 (P = 0.1085);Gain of phosphorylation at T1718 (P = 0.1085);.;
MVP
0.45
ClinPred
0.39
T
GERP RS
2.4
Varity_R
0.60
gMVP
0.68

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

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: chr7-21698453; API