5-179836445-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM1 BP4_Moderate BS2

The NM_003900.5(SQSTM1):c.1175C>T(p.Pro392Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00142 in 1,614,158 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P392P) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.0013 (1 hom., cov: 33)
  • Exomes 𝑓: 0.0014 (2 hom.)
• Consequence: SQSTM1 NM_003900.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:11 U:3
• Conservation: PhyloP100: 7.87

Genes affected

SQSTM1 (HGNC:11280): (sequestosome 1) This gene encodes a multifunctional protein that binds ubiquitin and regulates activation of the nuclear factor kappa-B (NF-kB) signaling pathway. The protein functions as a scaffolding/adaptor protein in concert with TNF receptor-associated factor 6 to mediate activation of NF-kB in response to upstream signals. Alternatively spliced transcript variants encoding either the same or different isoforms have been identified for this gene. Mutations in this gene result in sporadic and familial Paget disease of bone. [provided by RefSeq, Mar 2009]

MRNIP (HGNC:30817): (MRN complex interacting protein) Enables chromatin binding activity. Involved in several processes, including mitotic G2 DNA damage checkpoint signaling; regulation of double-strand break repair; and response to ionizing radiation. Located in nucleoplasm. Colocalizes with Mre11 complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 10 uncertain in NM_003900.5
• BP4: Computational evidence support a benign effect (MetaRNN=0.09615874).
• BS2: High AC in GnomAd at 203 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SQSTM1	NM_003900.5	c.1175C>T	p.Pro392Leu	missense_variant	8/8	ENST00000389805.9
SQSTM1	NM_001142298.2	c.923C>T	p.Pro308Leu	missense_variant	9/9
SQSTM1	NM_001142299.2	c.923C>T	p.Pro308Leu	missense_variant	9/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SQSTM1	ENST00000389805.9	c.1175C>T	p.Pro392Leu	missense_variant	8/8	1	NM_003900.5	P1
SQSTM1	ENST00000360718.5	c.923C>T	p.Pro308Leu	missense_variant	7/7	1
MRNIP	ENST00000522663.5	c.*1245G>A		3_prime_UTR_variant, NMD_transcript_variant	9/9	1
SQSTM1	ENST00000510187.5	c.951-26C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.00133 AC: 203 AN: 152154 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.000145

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00531

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00162

Gnomad OTH AF: 0.00192

GnomAD3 exomes AF: 0.000980 AC: 246 AN: 251018 Hom.: 2 AF XY: 0.000987 AC XY: 134 AN XY: 135722

Gnomad AFR exome AF: 0.000246

Gnomad AMR exome AF: 0.00127

Gnomad ASJ exome AF: 0.000198

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000294

Gnomad FIN exome AF: 0.000370

Gnomad NFE exome AF: 0.00145

Gnomad OTH exome AF: 0.00244

GnomAD4 exome AF: 0.00143 AC: 2091 AN: 1461886 Hom.: 2 Cov.: 31 AF XY: 0.00139 AC XY: 1013 AN XY: 727242

Gnomad4 AFR exome AF: 0.000179

Gnomad4 AMR exome AF: 0.00170

Gnomad4 ASJ exome AF: 0.000153

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000336

Gnomad4 FIN exome AF: 0.000300

Gnomad4 NFE exome AF: 0.00168

Gnomad4 OTH exome AF: 0.00156

GnomAD4 genome AF: 0.00133 AC: 203 AN: 152272 Hom.: 1 Cov.: 33 AF XY: 0.00138 AC XY: 103 AN XY: 74448

Gnomad4 AFR AF: 0.000144

Gnomad4 AMR AF: 0.00530

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00162

Gnomad4 OTH AF: 0.00190

Alfa AF: 0.00131 Hom.: 1

Bravo AF: 0.00196

TwinsUK AF: 0.00135 AC: 5

ALSPAC AF: 0.00104 AC: 4

ESP6500AA AF: 0.000227 AC: 1

ESP6500EA AF: 0.00209 AC: 18

ExAC AF: 0.000889 AC: 108

EpiCase AF: 0.00158

EpiControl AF: 0.00160

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:11 Uncertain:3

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:2 Uncertain:3

Likely pathogenic, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The SQSTM1 p.P392L variant is a well-known variant and was identified in 59 of 356 proband chromosomes (frequency: 0.1657) from individuals or families with Paget’s disease of bone (PDB) and was not identified in 582 control chromosomes from healthy individuals (Laurin_2002_PMID:11992264, Hocking_2002_PMID:12374763, Seton_2016_PMID:26713335). The p.P392L variant was also identified in patients with PDB in the Dutch, Italian, French-Canadian, and Australian populations and was also shown to segregate with disease in 20 families from Quebec with PDB (Laurin_2002_PMID:11992264; Morissette_2006_PMID:17229007; Hocking_2002_PMID:12374763; Eekhoff_2004_PMID:15146436; Falchetti_2004_PMID:15125799; Good_2004_PMID:15207768). In addition to Paget’s disease of bone, the p.P392L variant has been identified in patients with Amyotrophic Lateral Sclerosis (ALS), Frontotemporal Dementia (FTD), and Distal Myopathy (Fecto_2011_PMID:22084127, Teyssou_2013_PMID:23417734, Le Ber_2013_PMID:24042580, Kwok_2014_PMID:23942205, van der Zee_2014_PMID:24899140, Niu_2018_PMID:29599744). Some of these patients with ALS did not have a personal/family history of PDB or they did; one family had three affected individuals with FTD and PDB and other unaffected family members did not carry the variant (Fecto_2011_PMID:22084127, Le Ber_2013_PMID:24042580, Kwok_2014_PMID:23942205, Niu_2018_PMID:29599744). The p.P392L variant is located in the highly conserved ubiquitin-associated (UBA) domain in the p62 protein which is involved in multiubiquitin chain binding. An NMR structure of the UBA domain with the p.P392L mutant showed no effect on the interaction of the UBA domain with multiubiquitin chain binding (Ciani_2003_PMID:12857745). An in vitro assay showed the p.P392L mutation does not affect the binding properties of UBA, however it had subtle local effects on the UBA domain structure (Layfield_2004_PMID:15493999). Other in vitro functional expression studies in E. coli showed the p.P392L mutation caused loss of monoubiquitin binding and impaired K48-linked polyubiquitin binding (Cavey_2005_PMID:15765181). There are conflicting in vivo studies on mice with the p.P392L mutation and association with PDB (Hiruma_2008_PMID:18765443, Daroszewska_2011_PMID:21515589). Chamoux et al. conducted in vivo studies on mature osteoclasts from PDB patients and healthy donors that carried or do not carry the p.P392L variant. Results showed the p62 protein was significantly more expressed in PDB patient than in healthy donors, regardless of whether the p.P392L variant was present or not. However, overexpression of p.P392L mutated p62 led to the formation of more osteoclasts which contained more nuclei than non-transfected cells or cells overexpressing wild-type p62. The p62 p.P392L mutation contributed to increased activation of other proteins (Chamoux_2009_PMID:19589897). Other studies speculate environmental and genetics factors involved in the formation of disease in those with PDB and distal myopathy (Niu_2018_PMID:29599744, Kurihara_2011_PMID:21195346). The variant was identified in dbSNP (ID: rs104893941), LOVD 3.0 and ClinVar (conflicting interpretations of pathogenicity: uncertain significance by GeneDx, pathogenic by Laboratory for Molecular Medicine and Illumina, likely pathogenic by Division of Human Genetics, Children's Hospital of Philadelphia , and benign by Invitae, associated with the conditions Paget disease, Amyotrophic lateral sclerosis and/or frontotemporal dementia 1, and Frontotemporal dementia and/or amyotrophic lateral sclerosis 3). The variant was identified in control databases in 259 of 282398 chromosomes (2 homozygous) at a frequency of 0.000917 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: Other in 15 of 7228 chromosomes (freq: 0.002075), European (non-Finnish) in 173 of 128718 chromosomes (freq: 0.001344), La -
Likely pathogenic, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Sep 26, 2017	- -
Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Aug 01, 2023	SQSTM1: PS4:Moderate, PS3:Supporting -
Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Jun 09, 2023	PP3, PM1 -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	May 09, 2023	Observed in multiple unrelated patients with Paget disease of bone (PDB), frontotemporal dementia (FTD), and/or amyotrophic lateral sclerosis (ALS) in published literature (Almeida et al., 2016; Le Ber et al., 2013; McCann et al., 2020; Teyssou et al., 2013, Tripolszki et al., 2019; Acosta-Uribe et al. 2022); however, variant has been observed in controls; Published mouse models expressing the P392L equivalent variant (P394L in the murine sqstm1 gene) developed a skeletal disorder similar to PDB (Daroszewska et al., 2011); however studies using affected patient cells and a different mouse model suggest that the P392L variant may be insufficient to cause PDB on its own, and additional genetic and/or environmental factors may be required (Kurihara et al., 2011; Seton et al., 2016; Hiruma et al., 2008); 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: 24899140, 15493999, 18765443, 19589897, 12857745, 26713335, 28430856, 23942205, 25241215, 33612544, 32329415, 32893041, 33325387, 34426522, 11992264, 21195346, 26839080, 24042580, 32409511, 23417734, 33015249, 30889971, 31000212, 30729484, 30671590, 30726512, 31462833, 28889094, 32978683, 29457785, 27594680, 27275741, 29948344, 29599744, 30886882, 25708934, 30594595, 15125799, 26627873, 31634910, 31616248, 32176830, 31530427, 35241069, 35260199, 21515589, 31475037, 35229101, 36327984, 35769265, 35708843, 36918542, 35355568, 36035996, 35330074, 36133075) -

Paget disease of bone 3 Pathogenic:3

Pathogenic, no assertion criteria provided	literature only	OMIM	Sep 01, 2014	- -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 28, 2017	The SQSTM1 c.1175C>T (p.Pro392Leu) missense variant is the most commonly observed SQSTM1 variant in individuals with Paget disease of bone (PDB) to date (Seton et al. 2016). Across a selection of the literature, the p.Pro392Leu variant has been identified in a homozygous state in four PDB patients and in a heterozygous state in 101 individuals with familial PDB and in 211 individuals with sporadic PDB (Laurin et al. 2002; Michou et al. 2003; Hocking et al. 2004; Lucas et al. 2005; Morissette et al. 2006; Chung et al. 2008; Rea et al. 2009; Visconti et al. 2010; Seton et al. 2016). Morissette et al. (2006) calculated the penetrance of this variant to be 50% among all age groups, and approximately 80% for individuals over the age of 60. The p.Pro392Leu variant was absent from 1186 controls but is reported at a frequency of 0.02404 in the Puerto Ricans from Puerto Rico population of the 1000 Genomes Project. This frequency is high but is consistent with the disease prevalence and reduced penetrance seen among younger individuals. Several studies identified a shared ancestral haplotype among most individuals carrying the p.Pro392Leu variant allele, indicating that the variant is likely a founder mutation in populations of Western European descent (Laurin et al. 2002; Lucas et al. 2005; Morissette et al. 2006; Chung et al. 2008; Rea et al. 2009). Functional studies demonstrated that the p.Pro392Leu variant disrupted protein interaction and reduced binding affinity for ubiquitin (Cavey et al. 2005; Rea et al. 2006; Chamoux et al. 2009; Kurihara et al. 2011; Sundaram et al. 2011). Based on the collective evidence, the p.Pro392Leu variant is classified as pathogenic for Paget disease of bone. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Apr 29, 2019	- -

Frontotemporal dementia and/or amyotrophic lateral sclerosis 3 Pathogenic:2

Pathogenic, no assertion criteria provided	literature only	OMIM	Sep 01, 2014	- -
Pathogenic, criteria provided, single submitter	clinical testing	Centogene AG - the Rare Disease Company	Sep 20, 2021	- -

Frontotemporal dementia and/or amyotrophic lateral sclerosis 1;C4085251:Paget disease of bone 2, early-onset Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Jan 28, 2024

This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 392 of the SQSTM1 protein (p.Pro392Leu). This variant is present in population databases (rs104893941, gnomAD 0.1%), including at least one homozygous and/or hemizygous individual. This missense change has been observed in individual(s) with Paget disease of the bone (PMID: 11473345, 11992264, 15125799, 17229007). It has also been observed to segregate with disease in related individuals. The penetrance of this variant appears to be reduced and increases with age. In one study, the penetrance was 50% across all age groups but 17% below the age of 50 (PMID: 17229007). Of note, this variant has also been observed in individuals with frontotemporal dementia (PMID: 24899140, 24042580), amyotrophic lateral sclerosis (PMID:23417734, 23942205, 24899140, 28430856), and myopathy (PMID:29457785, 29599744), but the association with these diseases is unclear. ClinVar contains an entry for this variant (Variation ID: 8108). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on SQSTM1 protein function. Experimental studies have shown that this missense change affects SQSTM1 function (PMID: 15765181, 16813535, 19589897, 21195346, 21878516). For these reasons, this variant has been classified as Pathogenic. -

Amyotrophic lateral sclerosis Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Human Genetics Bochum, Ruhr University Bochum

Nov 10, 2022

ACMG criteria used to clasify this variant: PS4_MOD, PM1, PP3_MOD, PM2_SUP, BS2 -

Spastic paraplegia-Paget disease of bone syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Oct 09, 2018

The p.Pro392Leu variant in SQSTM1 has been reported in at least 100 individuals with Paget disease of the bone (PDB) and was found to segregate with PDB in >40 individuals across 11 families (Laurin 2002, Morissette 2006, Seton 2016). In vi tro and in vivo functional studies support an impact on protein function (Layfie ld 2004, Hiruma 2008, Chamoux 2009, Kurihara 2011; Daroszewska 2018); however, s ome of these studies suggest that the variant is not sufficient to cause disease on its own, and that environmental stimuli may play a role in its phenotypic ex pression (Hiruma 2008, Kurihara 2011). This variant has also been identified in 0.14% (179/126230) of European chromosomes by gnomAD, including 2 homozygous ind ividuals (http://gnomad.broadinstitute.org). This appreciable frequency is consi stent with the reduced penetrance of PDB as well as the high prevalence of PDB i n European populations (estimates range from 0.2-10% across different patient po pulations; Morrisette 2006, Valenzuela 2017). It should be noted that this varia nt has also been reported in patients with frontotemporal dementia (FTD; van der Zee 2014, Le Ber 2013), amyotrophic lateral sclerosis (ALS; Teyssou 2013, Kwok 2014, van der Zee 2014, Morgan 2017), and myopathy (Lee 2018, Niu 2018). However , the role of the SQSTM1 gene in these disorders is not well established. In sum mary, the p.Pro392Leu variant meets criteria to be classified as pathogenic for PDB in an autosomal dominant manner with reduced penetrance. Additional data is required to determine if this variant contributes to other disorders. -

Paget disease of bone 3;C4225326:Frontotemporal dementia and/or amyotrophic lateral sclerosis 3 Pathogenic:1

Likely pathogenic, no assertion criteria provided

research

Division of Human Genetics, Children's Hospital of Philadelphia

Jun 23, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.42
BayesDel_addAF	Uncertain	0.077	D
BayesDel_noAF	Pathogenic	0.31
Cadd	Pathogenic	29
Dann	Uncertain	1.0
DEOGEN2	Pathogenic	0.93	D;.
Eigen	Uncertain	0.42
Eigen_PC	Uncertain	0.44
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Uncertain	0.95	D;D
MetaRNN	Benign	0.096	T;T
MetaSVM	Uncertain	0.58	D
MutationAssessor	Benign	1.7	L;.
MutationTaster	Benign	1.0	A;A;A;A;A;A
PrimateAI	Uncertain	0.74	T
PROVEAN	Pathogenic	-6.9	D;D
REVEL	Pathogenic	0.82
Sift	Uncertain	0.0020	D;D
Sift4G	Benign	0.070	T;T
Polyphen		0.99	D;.
Vest4		0.92
MVP		0.99
MPC		0.59
ClinPred		0.13	T
GERP RS		4.8
Varity_R		0.72
gMVP		0.51

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: rs104893941; hg19: chr5-179263445; COSMIC: COSV52972727; COSMIC: COSV52972727;