7-47846960-C-G
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PP3_StrongPP5_Moderate
The NM_138295.5(PKD1L1):c.5072G>C(p.Cys1691Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000112 in 1,613,904 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
PKD1L1
NM_138295.5 missense
NM_138295.5 missense
Scores
8
8
3
Clinical Significance
Conservation
PhyloP100: 4.80
Genes affected
PKD1L1 (HGNC:18053): (polycystin 1 like 1, transient receptor potential channel interacting) This gene encodes a member of the polycystin protein family containing 11 transmembrane domains, a receptor for egg jelly (REJ) domain, and a polycystin-1, lipoxygenase, alpha-toxin (PLAT) domain. The encoded protein may play a role in the male reproductive system. Alternative splice variants have been described but their biological nature has not been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.944
PP5
?
Variant 7-47846960-C-G is Pathogenic according to our data. Variant chr7-47846960-C-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 235198.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKD1L1 | NM_138295.5 | c.5072G>C | p.Cys1691Ser | missense_variant | 32/57 | ENST00000289672.7 | |
PKD1L1 | XM_017011798.3 | c.5249G>C | p.Cys1750Ser | missense_variant | 33/59 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKD1L1 | ENST00000289672.7 | c.5072G>C | p.Cys1691Ser | missense_variant | 32/57 | 1 | NM_138295.5 | P2 | |
PKD1L1 | ENST00000690269.1 | c.5072G>C | p.Cys1691Ser | missense_variant | 32/58 | A2 | |||
PKD1L1 | ENST00000685709.1 | c.4904G>C | p.Cys1635Ser | missense_variant | 31/56 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152232Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461672Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727122
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ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Situs inversus Pathogenic:1
Likely pathogenic, criteria provided, single submitter | research | Baylor Genetics | May 27, 2016 | Pathogenicity based on finding the variant in the homozygous state in a female with situs inversus totalis and congenital heart defect. - |
Heterotaxy, visceral, 8, autosomal Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 14, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Uncertain
D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Pathogenic
D
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Pathogenic
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MutPred
Loss of sheet (P = 0.0104);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at