rs199504211

Positions:

• chr12-106427339-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP2 PP5

The NM_018082.6(POLR3B):​c.1244T>C​(p.Met415Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000871 in 1,613,792 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.00064 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00089 (1 hom.)
• Consequence: POLR3B NM_018082.6 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:8 U:9 O:1
• Conservation: PhyloP100: 7.52

Genes affected

POLR3B (HGNC:30348): (RNA polymerase III subunit B) This gene encodes the second largest subunit of RNA polymerase III, the polymerase responsible for synthesizing transfer and small ribosomal RNAs in eukaryotes. The largest subunit and the encoded protein form the catalytic center of RNA polymerase III. Mutations in this gene are a cause of hypomyelinating leukodystrophy. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), POLR3B. . Gene score misZ 3.1978 (greater than the threshold 3.09). Trascript score misZ 3.4842 (greater than threshold 3.09). GenCC has associacion of gene with hypomyelination-hypogonadotropic hypogonadism-hypodontia syndrome, Charcot-Marie-Tooth disease, demyelinating, IIA 1I, hypomyelinating leukodystrophy 8 with or without oligodontia and-or hypogonadotropic hypogonadism, endosteal sclerosis-cerebellar hypoplasia syndrome.
• PP5: Variant 12-106427339-T-C is Pathogenic according to our data. Variant chr12-106427339-T-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 285205.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=8, Pathogenic=3, not_provided=1, Likely_pathogenic=5}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POLR3B	NM_018082.6	c.1244T>C	p.Met415Thr	missense_variant	13/28	ENST00000228347.9	NP_060552.4
POLR3B	NM_001160708.2	c.1070T>C	p.Met357Thr	missense_variant	13/28		NP_001154180.1
POLR3B	XM_017019621.3	c.1244T>C	p.Met415Thr	missense_variant	13/26		XP_016875110.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POLR3B	ENST00000228347.9	c.1244T>C	p.Met415Thr	missense_variant	13/28	1	NM_018082.6	ENSP00000228347.4
POLR3B	ENST00000539066.5	c.1070T>C	p.Met357Thr	missense_variant	13/28	2		ENSP00000445721.1
POLR3B	ENST00000549569.1	c.*9T>C		downstream_gene_variant		4		ENSP00000448398.1

Frequencies

GnomAD3 genomes AF: 0.000644 AC: 98 AN: 152210 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00134

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000554 AC: 139 AN: 251068 Hom.: 0 AF XY: 0.000553 AC XY: 75 AN XY: 135658

Gnomad AFR exome AF: 0.000123

Gnomad AMR exome AF: 0.0000579

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000924

Gnomad NFE exome AF: 0.00115

Gnomad OTH exome AF: 0.000490

GnomAD4 exome AF: 0.000895 AC: 1308 AN: 1461464 Hom.: 1 Cov.: 32 AF XY: 0.000851 AC XY: 619 AN XY: 727058

Gnomad4 AFR exome AF: 0.000120

Gnomad4 AMR exome AF: 0.0000447

Gnomad4 ASJ exome AF: 0.0000383

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000936

Gnomad4 NFE exome AF: 0.00114

Gnomad4 OTH exome AF: 0.000497

GnomAD4 genome AF: 0.000643 AC: 98 AN: 152328 Hom.: 0 Cov.: 32 AF XY: 0.000510 AC XY: 38 AN XY: 74494

Gnomad4 AFR AF: 0.000120

Gnomad4 AMR AF: 0.000131

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00134

Gnomad4 OTH AF: 0.00

Alfa AF: 0.00115 Hom.: 0

Bravo AF: 0.000578

TwinsUK AF: 0.00135 AC: 5

ALSPAC AF: 0.000778 AC: 3

ESP6500AA AF: 0.000227 AC: 1

ESP6500EA AF: 0.00105 AC: 9

ExAC AF: 0.000618 AC: 75

EpiCase AF: 0.00158

EpiControl AF: 0.000771

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:8 Uncertain:9 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:3 Uncertain:3

Likely pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jun 01, 2023	POLR3B: PM3:Strong, PM2, PP2 -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 11, 2024	In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 35316923, 27512013, 33726816, 34440436, 32870266, 36268624, 37273706, 27029625, 25133958, 32345981, 22855961) -
Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	May 30, 2018	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 24, 2024	This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 415 of the POLR3B protein (p.Met415Thr). This variant is present in population databases (rs199504211, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with clinical features of autosomal recessive POLR3B-related conditions (PMID: 25133958, 27029625, 27512013, 34440436). ClinVar contains an entry for this variant (Variation ID: 285205). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt POLR3B protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Oct 23, 2020	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Jul 12, 2024	BS1, PP3, PM3_strong -

Hypomyelinating leukodystrophy 8 with or without oligodontia and-or hypogonadotropic hypogonadism Pathogenic:3 Uncertain:2 Other:1

Uncertain significance, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Oct 31, 2022	- -
not provided, no classification provided	literature only	GeneReviews	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Undiagnosed Diseases Network, NIH	May 30, 2022	- -
Uncertain significance, criteria provided, single submitter	curation	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	Jan 24, 2023	The p.Met415Thr variant in POLR3B has been reported in 7 individuals with 4H leukodystrophy (PMID: 27512013, 25133958, 27029625, 33726816, 34440436, 31996231) and has been identified in 0.11% (149/128840) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs199504211). 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#: 285205) and has been interpreted as VUS by Eurofins NTD (LLC) and Fulgent Genetics, and likely pathogenic or pathogenic by Institute of Human Genetics (University of Leipzig Medical Center), Institute of Medical Genetics and Applied Genomics (University Hospital Tübingen), GeneDx, and GeneReviews. Of the 7 affected individuals, 2 were compound heterozygotes that carried reported pathogenic variants in trans and with unknown phase, which increases the likelihood that the p.Met415Thr variant is pathogenic (VariationID: 620581; PMID: 31996231, 27512013). Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. The number of missense variants reported in POLR3B in the general population is lower than expected, suggesting there is little benign variation in this gene and slightly increasing the possibility that a missense variant in this gene may not be tolerated. In summary, the clinical significance of the p.Met415Thr variant is uncertain. ACMG/AMP Criteria applied: PP3, PM3, PP2 (Richards 2015). -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Feb 21, 2021	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Jan 01, 2019	- -

Inborn genetic diseases Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 04, 2022

The c.1244T>C (p.M415T) alteration is located in exon 13 (coding exon 13) of the POLR3B gene. This alteration results from a T to C substitution at nucleotide position 1244, causing the methionine (M) at amino acid position 415 to be replaced by a threonine (T)._x000D_ _x000D_ Based on the available evidence, the c.1244T>C p.M415T alteration is classified as likely pathogenic for autosomal recessive POLR3B-related hypomyelinating leukodystrophy; however, it is unlikely to be causative of autosomal dominant POLR3B-related Charcot-Marie-Tooth disease type 1. Based on data from gnomAD, the C allele has an overall frequency of 0.06% (160/282446) total alleles studied. The highest observed frequency was 0.12% (149/128840) of European (non-Finnish) alleles. This variant has been reported to be compound heterozygous with other POLR3B variants in multiple individuals with features consistent with POLR3B-related hypomyelinating leukodystrophy (Fogel, 2014; La Piana, 2016; Richards, 2017; Barbosa-Gouveia, 2021; Gach, 2022). This amino acid position is highly conserved in available vertebrate species. The in silico prediction for this alteration is inconclusive. Based on the available evidence, this alteration is classified as likely pathogenic. -

See cases Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein

Nov 16, 2020

ACMG classification criteria: PS4, PM3, PP3 -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

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

Mar 13, 2023

Variant summary: POLR3B c.1244T>C (p.Met415Thr) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00055 in 251068 control chromosomes. c.1244T>C has been reported in the literature in individuals affected with POLR3-Related Leukodystrophy, cerebellar ataxia, isolated hypogonadotropic hypogonadism (Barbosa-Gouveia_2021, Fogel_2014, Richards_2017) and in an individual with clinical features of ataxia, myopia, developmental delay, short stature, and cerebellar atrophy (La Piana_2016). In all cases, the second allele reported in the patients were of unknown or uncertain significance. These reports do not provide unequivocal conclusions about association of the variant with POLR3-Related Leukodystrophy. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. 11 ClinVar submitters have submitted clinical-significance assessments for this variant to ClinVar after 2014. Multiple laboratories reported the variant with conflicting assessments including uncertain significance (n=5), likely pathogenic (n=4), or pathogenic (n=2). Based on the evidence outlined above, the variant was classified as uncertain significance. -

Amenorrhea Uncertain:1

Uncertain significance, no assertion criteria provided

literature only

Yale Center for Mendelian Genomics, Yale University

Mar 08, 2021

- -

POLR3-related leukodystrophy Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Sep 14, 2023

The POLR3B c.1244T>C (p.Met415Thr) missense variant has been reported in at least five individuals with variable presentations of POLR3-related conditions, including ataxia, hypogonadotropic hypogonadism, white matter abnormalities on brain MRI, and myopia (PMID: 25133958; 27029625; 27512013; 33726816; 34440436). In two of these cases, the variant co-occurred with a predicted loss of function variant, and in at least three other cases it has been reported in trans with another missense variant. The highest frequency of this allele in the Genome Aggregation Database is 0.001337 in the European (non-Finnish) population (version 3.1.2). Computational evidence suggests the variant may impact the gene or gene product. Based on the available evidence, the c.1244T>C (p.Met415Thr) variant is classified as a variant of uncertain significance for POLR3-related leukodystrophy. -

Hypogonadotropic hypogonadism 7 with or without anosmia;C3280644:Hypomyelinating leukodystrophy 8 with or without oligodontia and-or hypogonadotropic hypogonadism;C4706676:Leukoencephalopathy, ataxia, hypodontia, hypomyelination syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 31, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.92
BayesDel_addAF	Benign	-0.092	T
BayesDel_noAF	Uncertain	0.050
CADD	Pathogenic	26
DANN	Uncertain	0.99
DEOGEN2	Benign	0.31	T;.
Eigen	Uncertain	0.51
Eigen_PC	Uncertain	0.59
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Pathogenic	0.98	D;D
M_CAP	Pathogenic	0.32	D
MetaRNN	Uncertain	0.59	D;D
MetaSVM	Uncertain	-0.23	T
MutationAssessor	Uncertain	2.1	M;.
PrimateAI	Pathogenic	0.91	D
PROVEAN	Uncertain	-2.9	D;D
REVEL	Pathogenic	0.82
Sift	Uncertain	0.0010	D;D
Sift4G	Uncertain	0.0020	D;D
Polyphen		0.42	B;.
Vest4		0.98
MVP		0.78
MPC		1.1
ClinPred		0.13	T
GERP RS		5.8
Varity_R		0.71
gMVP		0.91

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

LitVar

Other links and lift over

dbSNP: rs199504211; hg19: chr12-106821117; COSMIC: COSV99075432; COSMIC: COSV99075432;