chr6-52079950-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_138694.4(PKHD1):​c.340C>G​(p.Gln114Glu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

PKHD1
NM_138694.4 missense

Scores

4
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.29
Variant links:
Genes affected
PKHD1 (HGNC:9016): (PKHD1 ciliary IPT domain containing fibrocystin/polyductin) The protein encoded by this gene is predicted to have a single transmembrane (TM)-spanning domain and multiple copies of an immunoglobulin-like plexin-transcription-factor domain. Alternative splicing results in two transcript variants encoding different isoforms. Other alternatively spliced transcripts have been described, but the full length sequences have not been determined. Several of these transcripts are predicted to encode truncated products which lack the TM and may be secreted. Mutations in this gene cause autosomal recessive polycystic kidney disease, also known as polycystic kidney and hepatic disease-1. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.40601295).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PKHD1NM_138694.4 linkc.340C>G p.Gln114Glu missense_variant 5/67 ENST00000371117.8 NP_619639.3 P08F94-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PKHD1ENST00000371117.8 linkc.340C>G p.Gln114Glu missense_variant 5/671 NM_138694.4 ENSP00000360158.3 P08F94-1
PKHD1ENST00000340994.4 linkc.340C>G p.Gln114Glu missense_variant 5/615 ENSP00000341097.4 P08F94-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
29
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.077
BayesDel_addAF
Uncertain
0.036
T
BayesDel_noAF
Benign
-0.19
CADD
Benign
17
DANN
Benign
0.50
DEOGEN2
Benign
0.20
T;.
Eigen
Benign
0.12
Eigen_PC
Benign
0.15
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Benign
0.49
T;T
M_CAP
Benign
0.062
D
MetaRNN
Benign
0.41
T;T
MetaSVM
Benign
-0.40
T
MutationAssessor
Uncertain
2.7
M;M
PrimateAI
Benign
0.32
T
PROVEAN
Benign
-1.1
N;N
REVEL
Benign
0.29
Sift
Uncertain
0.028
D;T
Sift4G
Benign
0.30
T;T
Polyphen
0.90
P;B
Vest4
0.44
MutPred
0.43
Loss of sheet (P = 0.007);Loss of sheet (P = 0.007);
MVP
0.97
MPC
0.074
ClinPred
0.38
T
GERP RS
5.3
Varity_R
0.18
gMVP
0.46

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: chr6-51944748; API