chr6-52024676-C-T

Position:

• chr6-52024676-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 5P and 1B. PM1 PM2 PP5 BP4

The NM_138694.4(PKHD1):​c.5134G>A​(p.Gly1712Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000851 in 1,614,140 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00056 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00088 (0 hom.)
• Consequence: PKHD1 NM_138694.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:5 U:6 B:1
• Conservation: PhyloP100: 3.61

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM1: In a domain IPT/TIG 12; atypical (size 84) in uniprot entity PKHD1_HUMAN there are 18 pathogenic changes around while only 5 benign (78%) in NM_138694.4
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 6-52024676-C-T is Pathogenic according to our data. Variant chr6-52024676-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 286651.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=6, Likely_pathogenic=4, Likely_benign=1, Pathogenic=1}. Variant chr6-52024676-C-T is described in Lovd as [Pathogenic].
• BP4: Computational evidence support a benign effect (MetaRNN=0.30957827). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PKHD1	NM_138694.4	c.5134G>A	p.Gly1712Arg	missense_variant	32/67	ENST00000371117.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PKHD1	ENST00000371117.8	c.5134G>A	p.Gly1712Arg	missense_variant	32/67	1	NM_138694.4	P2
PKHD1	ENST00000340994.4	c.5134G>A	p.Gly1712Arg	missense_variant	32/61	5		A2

Frequencies

GnomAD3 genomes AF: 0.000572 AC: 87 AN: 152152 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000654

Gnomad ASJ AF: 0.00231

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000926

Gnomad OTH AF: 0.00335

GnomAD3 exomes AF: 0.000740 AC: 186 AN: 251314 Hom.: 0 AF XY: 0.000736 AC XY: 100 AN XY: 135818

Gnomad AFR exome AF: 0.000123

Gnomad AMR exome AF: 0.000665

Gnomad ASJ exome AF: 0.00496

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000131

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000898

Gnomad OTH exome AF: 0.000815

GnomAD4 exome AF: 0.000881 AC: 1288 AN: 1461870 Hom.: 0 Cov.: 34 AF XY: 0.000858 AC XY: 624 AN XY: 727240

Gnomad4 AFR exome AF: 0.000149

Gnomad4 AMR exome AF: 0.000738

Gnomad4 ASJ exome AF: 0.00517

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000232

Gnomad4 FIN exome AF: 0.0000187

Gnomad4 NFE exome AF: 0.000915

Gnomad4 OTH exome AF: 0.000960

GnomAD4 genome AF: 0.000565 AC: 86 AN: 152270 Hom.: 0 Cov.: 32 AF XY: 0.000322 AC XY: 24 AN XY: 74474

Gnomad4 AFR AF: 0.000120

Gnomad4 AMR AF: 0.0000654

Gnomad4 ASJ AF: 0.00231

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000415

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000926

Gnomad4 OTH AF: 0.00284

Alfa AF: 0.00121 Hom.: 1

Bravo AF: 0.000691

TwinsUK AF: 0.00108 AC: 4

ALSPAC AF: 0.000778 AC: 3

ESP6500AA AF: 0.000227 AC: 1

ESP6500EA AF: 0.00163 AC: 14

ExAC AF: 0.000700 AC: 85

Asia WGS AF: 0.000289 AC: 1 AN: 3478

EpiCase AF: 0.00153

EpiControl AF: 0.00101

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:5 Uncertain:6 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Autosomal recessive polycystic kidney disease Pathogenic:2 Uncertain:1 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	The PKHD1 c.5134G>A (p.Gly1712Arg) variant has been reported in three studies in which it is found in a compound heterozygous state with a frameshift variant in one individual with polycystic kidney disease (Gunay-Aygun et al. 2010). The p.Gly1712Arg variant was absent from 400 control chromosomes and is reported at a frequency of 0.00163 in the European American population of the Exome Sequencing Project. The evidence for this variant is limited. Therefore, the p.Gly1712Arg variant is classified as a variant of unknown significance but suspicious for pathogenicity for autosomal recessive polycystic kidney disease. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Counsyl	Oct 28, 2016	- -
Likely benign, criteria provided, single submitter	clinical testing	Invitae	Jan 30, 2024	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Apr 18, 2024	Variant summary: PKHD1 c.5134G>A (p.Gly1712Arg) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00074 in 251314 control chromosomes (gnomAD v2.1). This frequency is not higher than the estimated maximum expected for a pathogenic variant in PKHD1 causing Polycystic Kidney And Hepatic Disease (0.0071), allowing no conclusion about variant significance. c.5134G>A has been reported in the literature in multiple compound heterozygous individuals affected with Polycystic Kidney And Hepatic Disease (e.g. Gunay-Aygun_2010, Denamur_2010, Bullich_2018, Schueler_2016, Baldridge_2017, Mallawaarachchi_2021, El Naofal_2023), and several of these cases were reported to carry a pathogenic variant in trans. These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. ClinVar contains an entry for this variant (Variation ID: 286651). Based on the evidence outlined above, the variant was classified as pathogenic. -

not provided Pathogenic:1 Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Oct 29, 2019	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Apr 24, 2018	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Sep 28, 2016	The G1712R variant in the PKHD1 gene has been reported previously, along with a second mutation, in an individual with ARPKD (Gunay-Aygun et al., 2010). Although not present in the homozygous state, the NHLBI Exome Sequencing Project reports G1712R was observed in 14/8600 alleles from individuals of European background, indicating it may be a rare variant in this population. The G1712R variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. The G1712R variant is a strong candidate for a pathogenic variant, however the possibility it may be a rare benign variant cannot be excluded. -
Uncertain significance, criteria provided, single submitter	clinical testing	Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research	Jan 01, 2019	- -

Polycystic kidney disease 4 Pathogenic:1 Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 22, 2021	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Mar 30, 2024	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital	Aug 18, 2020	- -

PKHD1-related disorder Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Dec 01, 2023

The PKHD1 c.5134G>A variant is predicted to result in the amino acid substitution p.Gly1712Arg. Along with a pathogenic frameshift PKHD1 variant, the c.5134G>A (p.Gly1712Arg) variant has been reported in a patient with polycystic kidney disease (PKD) diagnosed at 28 years of age (Gunay-Aygun et al. PubMed ID: 19914852; Gunay-Aygun et al. PubMed ID: 20413436). This variant was also described in several other patients with polycystic kidney disease; these patients each harbored a known or potentially causative second variant in PKHD1 (Bullich et al. 2018. PubMed ID: 29801666, Supplementary Table 1; Schueler et al. 2016. PubMed ID: 26673778, Supplementary Table 2; Denamur et al. 2010. PubMed ID: 19940839, Table S2) and this variant has been identified in at least one ARPKD (autosomal recessive polycystic kidney disease) patient with a second PKHD1 variant at PreventionGenetics. This variant is reported in 0.48% of alleles in individuals of Ashkenazi Jewish descent in gnomAD. This variant is interpreted as likely pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.20
BayesDel_addAF	Pathogenic	0.17	D
BayesDel_noAF	Pathogenic	0.41
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.83	D;.
Eigen	Uncertain	0.38
Eigen_PC	Uncertain	0.27
FATHMM_MKL	Uncertain	0.90	D
LIST_S2	Uncertain	0.89	D;D
M_CAP	Pathogenic	0.52	D
MetaRNN	Benign	0.31	T;T
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Uncertain	2.8	M;M
MutationTaster	Benign	0.93	D;D
PrimateAI	Uncertain	0.50	T
PROVEAN	Pathogenic	-7.6	D;D
REVEL	Pathogenic	0.77
Sift	Pathogenic	0.0	D;D
Sift4G	Uncertain	0.0060	D;D
Polyphen		1.0	D;D
Vest4		0.87
MutPred		0.84		Gain of solvent accessibility (P = 0.0014);Gain of solvent accessibility (P = 0.0014);
MVP		0.96
MPC		0.18
ClinPred		0.67	D
GERP RS		4.7
Varity_R		0.67
gMVP		0.77

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs141103838; hg19: chr6-51889474;