chr17:44352876:C>T Detail (hg38) (GRN)

Information

Genome

Assembly Position
hg19 chr17:42,430,244-42,430,244 View the variant detail on this assembly version.
hg38 chr17:44,352,876-44,352,876

HGVS

Type Transcript Protein
RefSeq NM_002087.3:c.*78C>T
Ensemble ENST00000053867.8:c.*78C>T
ENST00000589265.5:c.*78C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.280
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 138945 OMIM
HGNC 4601 HGNC
Ensembl ENSG00000030582 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv57885770 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
risk factor 2008-12-01 no assertion criteria provided FRONTOTEMPORAL LOBAR DEGENERATION WITH UBIQUITIN-POSITIVE INCLUSIONS, SUSCEPTIBILITY TO germline Detail
Benign 2018-03-06 criteria provided, single submitter Grn-related frontotemporal lobar degeneration with Tdp43 inclusions germline Detail
Benign 2024-01-15 criteria provided, single submitter Grn-related frontotemporal lobar degeneration with Tdp43 inclusions,neuronal ceroid lipofuscinosis 11 germline Detail
Benign 2024-01-15 criteria provided, single submitter Grn-related frontotemporal lobar degeneration with Tdp43 inclusions,neuronal ceroid lipofuscinosis 11 germline Detail
Affects no assertion criteria provided Ischemic stroke somatic Detail
Benign 2018-06-19 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Hippocampal sclerosis For SNPs previously linked to hippocampal sclerosis, meta-analyses of Stage I re... BeFree 24770881 Detail
<0.001 Pick Disease of the Brain This is consistent with the finding that miR-659 binding to the high risk T alle... BeFree 21047645 Detail
0.001 Hippocampal sclerosis GRN rs5848 T-allele but not APOE ε4 was associated with HpScl. BeFree 21346515 Detail
<0.001 Hippocampal sclerosis GRN rs5848 T-allele but not APOE ε4 was associated with HpScl. BeFree 21346515 Detail
0.009 amyotrophic lateral sclerosis The purpose of this meta-analysis was to investigate the association between pro... BeFree 25578179 Detail
0.035 frontotemporal dementia A single nucleotide polymorphism (rs5848) located in the 3'- untranslated region... BeFree 19847305 Detail
0.179 Frontotemporal Lobar Degeneration A single nucleotide polymorphism (rs5848) located in the 3'- untranslated region... BeFree 19847305 Detail
0.003 dementia This is consistent with the finding that miR-659 binding to the high risk T alle... BeFree 21047645 Detail
0.034 Alzheimer's disease Similarly, the mRNA levels of granulin were decreased with respect to A allele o... BeFree 22890097 Detail
0.018 Neurodegenerative Disorders To assess the influence of rs5848 and rs646776 polymorphisms in both serum GRN l... BeFree 23398167 Detail
0.282 frontotemporal dementia A single nucleotide polymorphism (rs5848) located in the 3'- untranslated region... BeFree 19847305 Detail
<0.001 frontotemporal dementia This is consistent with the finding that miR-659 binding to the high risk T alle... BeFree 21047645 Detail
0.282 frontotemporal dementia This is consistent with the finding that miR-659 binding to the high risk T alle... BeFree 21047645 Detail
0.173 Frontotemporal Lobar Degeneration A single nucleotide polymorphism GRN rs5848 (3'UTR+78 C&gt;T) was reported to al... BeFree 23342160 Detail
0.282 frontotemporal dementia A single nucleotide polymorphism in the 3'-untranslated region of the progranuli... BeFree 19473366 Detail
0.442 FRONTOTEMPORAL LOBAR DEGENERATION WITH TDP43 INCLUSIONS, GRN-RELATED A single nucleotide polymorphism in the 3'-untranslated region of the progranuli... BeFree 19473366 Detail
0.194 dementia This is consistent with the finding that miR-659 binding to the high risk T alle... BeFree 21047645 Detail
0.173 Frontotemporal Lobar Degeneration The purpose of this meta-analysis was to investigate the association between pro... BeFree 25578179 Detail
0.006 Parkinson disease Our data indicate that rs5848 is associated with risk of AD and PD, suggesting i... BeFree 25578179 Detail
0.021 GRN-related frontotemporal dementia A single nucleotide polymorphism GRN rs5848 (3'UTR+78 C&gt;T) was reported to al... BeFree 23342160 Detail
0.034 Alzheimer's disease The purpose of this meta-analysis was to investigate the association between pro... BeFree 25578179 Detail
0.018 Neurodegenerative Disorders Association of progranulin polymorphism rs5848 with neurodegenerative diseases: ... BeFree 25578179 Detail
0.173 Frontotemporal Lobar Degeneration No association of PGRN 3'UTR rs5848 in frontotemporal lobar degeneration. BeFree 19446372 Detail
0.001 Mild cognitive disorder To assess the influence of rs5848 and rs646776 polymorphisms in both serum GRN l... BeFree 23398167 Detail
0.027 Pick Disease of the Brain This is consistent with the finding that miR-659 binding to the high risk T alle... BeFree 21047645 Detail
0.021 GRN-related frontotemporal dementia No association of PGRN 3'UTR rs5848 in frontotemporal lobar degeneration. BeFree 19446372 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002087.4(GRN):c.*78C>T AND FRONTOTEMPORAL LOBAR DEGENERATION WITH UBIQUITIN-POSITIVE INCLUSIONS, ... ClinVar Detail
NM_002087.4(GRN):c.*78C>T AND GRN-related frontotemporal lobar degeneration with Tdp43 inclusions ClinVar Detail
NM_002087.4(GRN):c.*78C>T AND multiple conditions ClinVar Detail
NM_002087.4(GRN):c.*78C>T AND multiple conditions ClinVar Detail
NM_002087.4(GRN):c.*78C>T AND Ischemic stroke ClinVar Detail
NM_002087.4(GRN):c.*78C>T AND not provided ClinVar Detail
For SNPs previously linked to hippocampal sclerosis, meta-analyses of Stage I results show OR = 1.16... DisGeNET Detail
This is consistent with the finding that miR-659 binding to the high risk T allele of rs5848 may aug... DisGeNET Detail
GRN rs5848 T-allele but not APOE ε4 was associated with HpScl. DisGeNET Detail
GRN rs5848 T-allele but not APOE ε4 was associated with HpScl. DisGeNET Detail
The purpose of this meta-analysis was to investigate the association between progranulin polymorphis... DisGeNET Detail
A single nucleotide polymorphism (rs5848) located in the 3'- untranslated region of GRN has recently... DisGeNET Detail
A single nucleotide polymorphism (rs5848) located in the 3'- untranslated region of GRN has recently... DisGeNET Detail
This is consistent with the finding that miR-659 binding to the high risk T allele of rs5848 may aug... DisGeNET Detail
Similarly, the mRNA levels of granulin were decreased with respect to A allele of rs5848 in the infe... DisGeNET Detail
To assess the influence of rs5848 and rs646776 polymorphisms in both serum GRN level and risk for co... DisGeNET Detail
A single nucleotide polymorphism (rs5848) located in the 3'- untranslated region of GRN has recently... DisGeNET Detail
This is consistent with the finding that miR-659 binding to the high risk T allele of rs5848 may aug... DisGeNET Detail
This is consistent with the finding that miR-659 binding to the high risk T allele of rs5848 may aug... DisGeNET Detail
A single nucleotide polymorphism GRN rs5848 (3'UTR+78 C&gt;T) was reported to alter the risk for fro... DisGeNET Detail
A single nucleotide polymorphism in the 3'-untranslated region of the progranulin gene (GRN; 3'UTR+7... DisGeNET Detail
A single nucleotide polymorphism in the 3'-untranslated region of the progranulin gene (GRN; 3'UTR+7... DisGeNET Detail
This is consistent with the finding that miR-659 binding to the high risk T allele of rs5848 may aug... DisGeNET Detail
The purpose of this meta-analysis was to investigate the association between progranulin polymorphis... DisGeNET Detail
Our data indicate that rs5848 is associated with risk of AD and PD, suggesting important roles of pr... DisGeNET Detail
A single nucleotide polymorphism GRN rs5848 (3'UTR+78 C&gt;T) was reported to alter the risk for fro... DisGeNET Detail
The purpose of this meta-analysis was to investigate the association between progranulin polymorphis... DisGeNET Detail
Association of progranulin polymorphism rs5848 with neurodegenerative diseases: a meta-analysis. DisGeNET Detail
No association of PGRN 3'UTR rs5848 in frontotemporal lobar degeneration. DisGeNET Detail
To assess the influence of rs5848 and rs646776 polymorphisms in both serum GRN level and risk for co... DisGeNET Detail
This is consistent with the finding that miR-659 binding to the high risk T allele of rs5848 may aug... DisGeNET Detail
No association of PGRN 3'UTR rs5848 in frontotemporal lobar degeneration. DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs5848 dbSNP
Genome
hg38
Position
chr17:44,352,876-44,352,876
Variant Type
snv
Reference Allele
C
Alternative Allele
T
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs5848
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2803
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4698
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
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