rs778599933

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1_ModeratePP5_Very_Strong

The NM_002087.4(GRN):c.708+6_708+9del variant causes a splice donor, splice donor region, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000282 in 1,453,738 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★).

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.000028 ( 0 hom. )

Consequence

GRN
NM_002087.4 splice_donor, splice_donor_region, intron

Scores

Not classified

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:6

Conservation

PhyloP100: 7.22

Variant links:

Genes affected

GRN (HGNC:4601): (granulin precursor) Granulins are a family of secreted, glycosylated peptides that are cleaved from a single precursor protein with 7.5 repeats of a highly conserved 12-cysteine granulin/epithelin motif. The 88 kDa precursor protein, progranulin, is also called proepithelin and PC cell-derived growth factor. Cleavage of the signal peptide produces mature granulin which can be further cleaved into a variety of active, 6 kDa peptides. These smaller cleavage products are named granulin A, granulin B, granulin C, etc. Epithelins 1 and 2 are synonymous with granulins A and B, respectively. Both the peptides and intact granulin protein regulate cell growth. However, different members of the granulin protein family may act as inhibitors, stimulators, or have dual actions on cell growth. Granulin family members are important in normal development, wound healing, and tumorigenesis. [provided by RefSeq, Jul 2008]

GRN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 10 ACMG points.

PVS1

Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 0.06116723 fraction of the gene. Cryptic splice site detected, with MaxEntScore 5.3, offset of 0 (no position change), new splice context is: aacGTgagg. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.

PP5

Variant 17-44350800-CGTGA-C is Pathogenic according to our data. Variant chr17-44350800-CGTGA-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 586221.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRN	NM_002087.4 linkuse as main transcript	c.708+6_708+9del		splice_donor_variant, splice_donor_region_variant, intron_variant		ENST00000053867.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRN	ENST00000053867.8 linkuse as main transcript	c.708+6_708+9del		splice_donor_variant, splice_donor_region_variant, intron_variant		1	NM_002087.4	P1	P28799-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000798

AC:

AN:

250578

Hom.:

AF XY:

0.0000148

AC XY:

AN XY:

135550

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000177

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000282

AC:

AN:

1453738

Hom.:

AF XY:

0.0000221

AC XY:

AN XY:

723766

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000362

Gnomad4 OTH exome

AF:

0.0000166

GnomAD4 genome

Cov.:

Bravo

AF:

0.0000151

EpiCase

AF:

0.00

EpiControl

AF:

0.0000593

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Pathogenic:3

Likely pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Nov 01, 2017	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Jun 08, 2018	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Oct 27, 2022	Reported previously in a patient with Alzheimers disease; however, no further clinical information was provided (Guven et al., 2016); Published functional studies demonstrate that the variant causes aberrant RNA splicing and reduction in PGRN mRNA, most likely through NMD of the mutant mRNA (Skoglund et al., 2011); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 31914217, 20975516, 30475763, 30739198, 27859661, 24709683, 29256051, 32742620, 36264717, 27632209) -

Inborn genetic diseases

Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 24, 2018

The c.708+6_708+9delTGAG intronic variant, located in intron 6 of the GRN gene, results from a deletion of 4 nucleotides within intron 6 of the GRN gene. This variant was detected in two individuals with frontotemporal lobular degeneration (FTLD) with ubiquitin positive inclusions; analysis in one individual demonstrated a reduction in mRNA levels (83% of wild type) and aberrant splicing (Skoglund L et al. Alzheimer Dis Assoc Disord;25:173-8). In a second study, mRNA levels were 56% and 73%, respectively, in two individuals with FTLD with TAR DNAbinding protein 43-positive inclusions (Bit-Ivan EN et al. J. Neuropathol. Exp. Neurol., 2014 May;73:467-73). In one family, this variant segregated with dementia in 3 affected individuals (Galimberti D et al. Mov. Disord., 2017 03;32:476-478). These nucleotide positions are well conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is predicted to weaken the efficiency of the native splice donor site; however, direct evidence is unavailable. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

GRN-related frontotemporal lobar degeneration with Tdp43 inclusions;C3539123:Neuronal ceroid lipofuscinosis 11

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Dec 18, 2023

This sequence change falls in intron 7 of the GRN gene. It does not directly change the encoded amino acid sequence of the GRN protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs778599933, gnomAD 0.002%). This variant has been observed in individuals with autosomal dominant frontotemporal lobar degeneration (PMID: 20975516, 24709683, 27632209, 27859661). This variant is also known as IVS6+5_8delGTGA (g.101707_101710delGTGA) and g.1642_1645delTGAG (IVS7 + 1delTGAG). ClinVar contains an entry for this variant (Variation ID: 586221). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 7 and introduces a premature termination codon (PMID: 20975516). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -

GRN-related frontotemporal lobar degeneration with Tdp43 inclusions

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Molecular Genetics, Royal Melbourne Hospital

Mar 01, 2024

This sequence change in GRN is an intronic variant located in intron 7. The highest population minor allele frequency in the population database gnomAD v4.0 is 0.004% (40/1,104,774 alleles) in the European (non-Finnish) population. The prevalence of the variant in individuals with frontotemporal dementia (FTD) is significantly increased compared with the prevalence in controls (PMID: 20975516, 24709683, 27632209, 27859661, 30475763, 31914217, 36264717, 33141172; gnomAD v4.0). The variant has been reported to segregate with FTD in multiple families (PMID: 27859661, 24709683, 30475763). The results from an in silico splicing predictor (SpliceAI) indicate that this variant may impact splicing by disrupting the donor splice site of intron 7 of GRN. This prediction is confirmed by RNA studies in patient cells (PMID: 20975516). Furthermore, progranulin levels in the serum/brain were significantly reduced in individuals with the variant (PMID: 20975516, 24709683, 27859661, 30475763). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.6.1, this variant is classified as PATHOGENIC. Following criteria are met: PP1_Strong, PS4, PVS1. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.40

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.28

Position offset: -44

DS_DL_spliceai

0.40

Position offset: 0

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over