rs191875469

chr10-78009515-C-T

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 8P and 1B. PP5_Very_Strong BP4

The NM_007055.4(POLR3A):c.1909+22G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00241 in 1,614,202 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.0015 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0025 (10 hom.)
• Consequence: POLR3A NM_007055.4 intron
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:27 U:2 O:2
• Conservation: PhyloP100: -0.768

Genes affected

POLR3A (HGNC:30074): (RNA polymerase III subunit A) The protein encoded by this gene is the catalytic component of RNA polymerase III, which synthesizes small RNAs. The encoded protein also acts as a sensor to detect foreign DNA and trigger an innate immune response. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

• PP5: Variant 10-78009515-C-T is Pathogenic according to our data. Variant chr10-78009515-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 445922.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-78009515-C-T is described in Lovd as [Likely_benign]. Variant chr10-78009515-C-T is described in Lovd as [Likely_pathogenic].
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).. Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POLR3A	NM_007055.4	c.1909+22G>A		intron_variant		ENST00000372371.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POLR3A	ENST00000372371.8	c.1909+22G>A		intron_variant		1	NM_007055.4	P1

Frequencies

GnomAD3 genomes AF: 0.00154 AC: 235 AN: 152234 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000579

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000785

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.000282

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00276

Gnomad OTH AF: 0.00144

GnomAD3 exomes AF: 0.00137 AC: 345 AN: 251418 Hom.: 0 AF XY: 0.00140 AC XY: 190 AN XY: 135880

Gnomad AFR exome AF: 0.000615

Gnomad AMR exome AF: 0.000925

Gnomad ASJ exome AF: 0.000794

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000849

Gnomad FIN exome AF: 0.000277

Gnomad NFE exome AF: 0.00224

Gnomad OTH exome AF: 0.00130

GnomAD4 exome AF: 0.00250 AC: 3653 AN: 1461850 Hom.: 10 Cov.: 32 AF XY: 0.00243 AC XY: 1764 AN XY: 727226

Gnomad4 AFR exome AF: 0.000418

Gnomad4 AMR exome AF: 0.00127

Gnomad4 ASJ exome AF: 0.000536

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000846

Gnomad4 FIN exome AF: 0.000318

Gnomad4 NFE exome AF: 0.00302

Gnomad4 OTH exome AF: 0.00177

GnomAD4 genome AF: 0.00154 AC: 235 AN: 152352 Hom.: 0 Cov.: 32 AF XY: 0.00160 AC XY: 119 AN XY: 74498

Gnomad4 AFR AF: 0.000577

Gnomad4 AMR AF: 0.000784

Gnomad4 ASJ AF: 0.000865

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.000282

Gnomad4 NFE AF: 0.00276

Gnomad4 OTH AF: 0.00142

Alfa AF: 0.00238 Hom.: 0

Bravo AF: 0.00150

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:27 Uncertain:2 Other:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Leukoencephalopathy-ataxia-hypodontia-hypomyelination syndrome Pathogenic:8 Uncertain:1 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Pathogenic, criteria provided, single submitter	curation	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	Jan 24, 2024	The c.1909+22G>A variant in POLR3A has been reported in >10 individuals with POLR3A-related disorders (PMID: 28459997, 30323018), segregated with disease in 4 affected relatives from 2 families (PMID: 28459997), and has been identified in 0.2% (289/129138) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs191875469). Although this variant has been seen in the general population in a heterozygous state, its frequency is not high enough to rule out a pathogenic role. This variant has also been reported in ClinVar (Variation ID#: 445922) and has been interpreted as likely pathogenic or pathogenic by multiple laboratories, as well as a variant of uncertain significance by a few additional labs. Of the 18 affected individuals, 1 of those was a homozygote and 8 were compound heterozygotes that carried reported pathogenic and likely pathogenic variants in trans or with unknown phase, which increases the likelihood that the c.1909+22G>A variant is pathogenic (VariationID: 684773; PMID: 28459997). In vitro functional studies provide some evidence that the c.1909+22G>A variant may impact protein function (PMID: 28459997). However, these types of assays may not accurately represent biological function. This variant is located in the 3’ splice region. Computational tools do not suggest an impact to splicing. However, this information is not predictive enough to rule out pathogenicity. This variant was also detected in 1 homozygous and supposedly unaffected Palestinian individual (PMID:30323018). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive POLR3A-related disorders. ACMG/AMP Criteria applied: PS3_moderate, PM3_strong, PP1_strong (Richards 2015). -
Uncertain significance, flagged submission	clinical testing	Baylor Genetics	Sep 25, 2019	This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -
Likely pathogenic, no assertion criteria provided	clinical testing	Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS)	Apr 01, 2023	- -
Likely pathogenic, no assertion criteria provided	clinical testing	Genomics England Pilot Project, Genomics England	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München	Aug 25, 2023	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	Mar 26, 2024	- -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	May 06, 2021	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with leukodystrophy, hypomyelinating, 7, with or without oligodontia and/or hypogonadotropic hypogonadism (MIM#607694), Wiedemann-Rautenstrauch syndrome (MIM#264090) and POLR3A-related spastic ataxia (PMID: 31637490). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0210 - Splice site variant proven to affect splicing of the transcript with a known effect on protein sequence. Functional analysis of patient leucocyte-derived cDNA, has demonstrated that this variant results in the leaky inclusion of 19 nucleotides in intron 14. This results in a shift in the reading frame, and the production of a protein with a premature termination codon (p.Tyr637Cysfs*14), shown to be degraded by nonsense mediated decay (PMID: 28459997). (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (386 heterozygotes, 0 homozygotes). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant as been reported many times as pathogenic, and has been observed in at least 30 compound heterozygous individuals with limb and gait ataxia (ClinVar). It has also been observed in a homozygous individual with childhood-onset axonal neuropathy (PMID: 28459997), and segregated in another family with spastic ataxia and hypodontia, who had an additional pathogenic splice variant in cis (PMID: 33491183). (SP) 1207 - Parental origin of the variant is unresolved (by quad analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	-	The intronic variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.136%). Although in silico tools do not predict the variant to alter splicing and produce an abnormal transcript (SpliceAI: 0.10), a study showed that alternative splicing having the first 19 nucleotides of intron 14 included in the transcript resulted in a shift of the reading frame (PMID: 28459997). The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least 4 similarly affected unrelated individuals (PMID: 28459997, 30323018, 30847471). The variant has been reported to co-segregate with the disease in at least 3 similarly affected relatives/individuals in the the same family or similarly affected unrelated family (PMID: 28459997). The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000445922/PMID: 27029625). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -

not provided Pathogenic:8

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Oct 29, 2019	Identified in multiple unrelated patients with POLR3A-related disorders tested at GeneDx and in the published literature who had different pathogenic variants on the opposite allele (La Piana et al., 2016; Minnerop et al., 2017; Travaglini et al., 2018) Functional studies suggest this variant generates a "leaky" cryptic donor site that results in the inclusion of part of intron 14 (Minnerop et al., 2017) In silico analysis, which includes splice predictors and evolutionary conservation, supports a deleterious effect Observed in 0.1365% (386/282828 alleles) in large population cohorts (Lek et al., 2016). -
Likely pathogenic, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Jun 02, 2017	- -
Likely pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	This sequence change falls in intron 14 of the POLR3A gene. It does not directly change the encoded amino acid sequence of the POLR3A protein. This variant is present in population databases (rs191875469, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. This variant has been observed in individual(s) with clinical features of POLR3A-related leukodystrophies (PMID: 27029625, 28459997, 29691679, 30323018, 30847471, 31637490). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 445922). Studies have shown that this variant alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 28459997, 30323018). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Oct 23, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2024	POLR3A: PM3:Very Strong, PP1:Strong, PM2, PS3:Supporting -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Jan 11, 2024	- -

Neonatal pseudo-hydrocephalic progeroid syndrome Pathogenic:4

Likely pathogenic, criteria provided, single submitter	research	Tartaglia Lab, Genetics and Rare Diseases Research Division, Bambino Gesu' Children's Hospital	May 01, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genomic Research Center, Shahid Beheshti University of Medical Sciences	Dec 30, 2023	- -
Pathogenic, criteria provided, single submitter	research	Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris	Jan 04, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	-	- -

POLR3A-related disorder Pathogenic:3

Likely pathogenic, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	Feb 20, 2024	The POLR3A c.1909+22G>A variant is predicted to interfere with splicing. This variant has been reported in the homozygous and compound heterozygous states in multiple families with variable-onset ataxia with or without tremor (La Piana et al. 2016. PubMed ID: 27029625; Minnerop et al. 2017. PubMed ID: 28459997; Travaglini et al. 2018. PubMed ID: 29691679; D'Amore et al. 2018. PubMed ID: 30564185; Paolacci et al. 2018. PubMed ID: 30323018; Rydning et al. 2019. PubMed ID: 30847471; Infante et al. 2020. PubMed ID: 31637490; de Assis Pereira Matos et al. 2020. PubMed ID: 32373668; Ruggiero et al. 2020. PubMed ID: 33085208). Additional studies indicate that the c.1909+22G>A variant, which is postulated to be a hypomorphic variant, generates a novel cryptic splice donor site, leading to a frameshift and premature protein termination; the resulting transcript is subject to nonsense-mediated mRNA decay (Minnerop et al. 2017. PubMed ID: 28459997). The c.1909+22G>A variant is reported at a minor allele frequency of up to ~0.22% in one large continental population but is not reported in the homozygous state. Based on the available evidence, we classify the c.1909+22G>A variant as likely pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Variantyx, Inc.	Nov 07, 2022	This is a non-canonical splice variant in the POLR3A gene (OMIM 614258). Biallelic pathogenic variants in this gene have been associated with autosomal recessive POLR3A-related disorders. Functional studies demonstrate that this variant disrupts mRNA splicing leading to premature termination and nonsense-mediated mRNA decay (PMID: 28459997, 30323018) (PVS1). This variant has been reported in the homozygous or compound heterozygous state in many unrelated affected individuals (PMID: 28459997, 29691679, 30847471, 31637490) (PM3_Very Strong). This variant has been observed to segregate with disease in multiple affected families (PMID: 30847471, 31637490) (PP1_Strong). This variant has a 0.2763 % maximum allele frequency in non-founder control populations (https://gnomad.broadinstitute.org/). Based on the current evidence, this variant is classified as pathogenic for autosomal recessive POLR3A-related disorders. -
Pathogenic, criteria provided, single submitter	research	Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL)	Apr 27, 2023	- -

Inborn genetic diseases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 07, 2021

The c.1909+22G>A intronic alteration results from a G to A substitution 22 nucleotides after coding exon 14 of the POLR3A gene. The c.1909+22G>A alteration is a hypomorphic allele that has been reported in the homozygous state and in trans with a second loss of function alteration in multiple unrelated patients with an autosomal recessive spastic ataxic phenotype with mild dental involvement and hyperintensities along the superior cerebellar peduncles (Minnerop, 2017; Rydning, 2019; Morales-Rosado, 2020; de Assis Pereira Matos, 2020). This alteration has been shown to cosegregate with disease in one family with four affected siblings (Minnerop, 2017). In a case-control study, the c.1909+22G>A variant was significantly associated (P = 1.3 x 10-4, odds ratio = 3.11) with hereditary spastic paraplegia, cerebellar ataxia, and/or neuropathy cases compared to other disease phenotypes and healthy controls (Minnerop, 2017). In addition, the c.1909+22G>A alteration has been reported in cis with c.3337-11T>C in several patients with Wiedemann-Rautenstrauch syndrome who carried this complex allele in trans with a second loss of function alteration (Paolacci, 2018). This nucleotide position is not well conserved in available vertebrate species. Functional RNA studies of c.1909+22G>A demonstrated a mild effect on splicing due to activation of an out of frame cryptic splice site which resulted in partial intron 14 retention and a transcript that was partially degraded by nonsense mediated decay (Minnerop, 2017; Rydning, 2019; Morales-Rosado, 2020). RNA studies in two patients who harbored the complex allele [c.1909+22G>A; c.3337-11T>C] demonstrated that both variants resulted in aberrant splicing and thus the additive effect on splicing was proposed to be a greater loss of function allele associated with a more severe phenotype (Paolacci, 2018). In addition, another variant affecting the same splice site (c.1909+18G>A) also demonstrated aberrant splicing on functional studies (Bernard, 2011). In silico splice site analysis for this alteration is inconclusive. Based on the available evidence, this alteration is classified as pathogenic. -

Spastic ataxia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Molecular Genetics, Royal Melbourne Hospital

Apr 01, 2022

This sequence change in POLR3A is an intronic variant located in intron 14. The highest population minor allele frequency in gnomAD v2.1 is 0.2% (289/129,138 alleles) in the European (non-Finnish) population. This variant has been detected homozygous or compound heterozygous with a second allele in at least 19 individuals with spastic ataxia with/without dental abnormalities, segregating with disease in at least two of these families (PMID: 28459997). The results from multiple in silico splicing predictors (SpliceAI, MaxEntScan, NNSplice) are conflicting on whether this variant may impact splicing by creation of a de novo donor splice site of intron 14 of POLR3A. This prediction is confirmed by RT-PCR. The assay demonstrated that the variant impacts splicing by activation of a leaky cryptic donor site leading to 19 bp intron 14 inclusion (p.Tyr637Cysfs*14). The variant has been described as a hypomorph, because it leads to leaky cryptic donor activation and is not associated with the classic POLR3A-related leukodystrophy phenotype (PMID: 28459997). Based on the classification scheme RMH Modified ACMG Guidelines v1.5.1, this variant is classified as PATHOGENIC. Following criteria are met: PM3_VeryStrong, PP1_Strong, PS3_Supporting. -

POLR3A-related neurological disorders Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Mar 02, 2020

The POLR3A c.1909+22G>A variant is an intronic variant. Across a selection of the available literature, the c.1909+22G>A variant has been identified in at least 30 unrelated individuals in a compound heterozygous state, all presenting with limb and gait ataxia. Tremor in the upper and lower limbs, dental problems, myopia, dysarthria, and dysphagia were also noted in some of these individuals. In addition, brain MRIs showed hyperintensities along the cerebellar peduncles, cervical cord atrophy, and hypoplasia of the corpus callosum (Minnerop et al. 2017; Rydning et al. 2019; Infante et al. 2020). Mild hypomyelination was also observed in some affected individuals (Rydning et al. 2019). The c.1909+22G>A variant was also present one individual in a homozygous state, primarily presenting with childhood-onset axonal neuropathy, in addition to gait ataxia (Minnerop et al. 2017). At least seven families had multiple affected individuals with the variant in a compound heterozygous state (Minnerop et al. 2017; Rydning et al. 2019; Infante et al. 2020). Evaluation of PCR products from affected individuals and healthy controls indicated that the variant affects splicing of exon 14, although this effect may be incomplete. In addition, inhibition of nonsense medicated mRNA decay in fibroblasts from affected individuals suggested the aberrantly spliced transcript due to the c.1909+22G>A variant is subject to nonsense mediated decay. In addition, gene and protein expression were reduced in the presence of the variant compared to controls (Minnerop et al. 2017). The c.1909+22G>A variant is reported at a frequency of 0.002238 in the European (non-Finnish) population of the Genome Aggregation Database. Based on the collective evidence, the c.1909+22G>A variant is classified as pathogenic for POLR3A-related neurological disorders. -

Pol III-related leukodystrophy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Oct 24, 2023

Variant summary: POLR3A c.1909+22G>A is located at a position not widely known to affect splicing. Several computational tools predict a significant impact on normal splicing: One predict the variant weakens a canonical 5' donor site. Three predict the variant strengthens a cryptic 5' donor site. Functional studies suggest this variant activates a "leaky" cryptic donor site that results in the inclusion of part of intron 14, and the production of a protein with a premature termination codon (p.Tyr637Cysfs*14), shown to be degraded by nonsense mediated decay (Minnerop_2017, Paolacci_ 2018). c.1909+22G>A has been reported in the literature in homozygous state and in trans with a loss of function alteration in multiple unrelated patients affected with autosomal recessive spastic ataxic phenotype (Minnerop_ 2017). Additionally, it has also been reported in individuals affected with leukodystrophy (Macken_ 2022) and Wiedemann-Rautenstrauch syndrome (Paolacci_ 2018). These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 28459997, 30323018, 36344503). Eighteen submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as pathogenic/likely pathogenic (n=15) as well as uncertain significance (n=3). Based on the evidence outlined above, the variant was classified as pathogenic. -

not specified Uncertain:1

Uncertain significance, flagged submission

clinical testing

Genetic Services Laboratory, University of Chicago

May 30, 2018

- -

Neonatal pseudo-hydrocephalic progeroid syndrome;C2676243:Leukoencephalopathy-ataxia-hypodontia-hypomyelination syndrome;C3280644:Hypomyelinating leukodystrophy 8 with or without oligodontia and-or hypogonadotropic hypogonadism Other:1

not provided, no classification provided

phenotyping only

GenomeConnect, ClinGen

-

Variant classified as Pathogenic and reported on 09-15-2021 by Lab or GTR ID 506526. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	4.7
Dann	Benign	0.63
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		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: rs191875469; hg19: chr10-79769273;