chr1:103379918:G>A Detail (hg19) (COL11A1)

Information

Genome

Assembly Position
hg19 chr1:103,379,918-103,379,918
hg38 chr1:102,914,362-102,914,362 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001190709.1:c.3851C>T NP_001177638.1:p.Pro1284Leu
NM_080629.2:c.4004C>T NP_542196.2:p.Pro1335Leu
NM_080630.3:c.3620C>T NP_542197.3:p.Pro1207Leu
Summary

MGeND

Clinical significance Benign
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.680
ToMMo:0.652
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.689

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 120280 OMIM
HGNC 2186 HGNC
Ensembl ENSG00000060718 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv2610469 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign Centenarian germline MGS000068
(TMGS000140) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2016-12-20 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2021-07-22 criteria provided, multiple submitters, no conflicts Stickler syndrome type 2 germline Detail
Benign 2021-07-22 criteria provided, multiple submitters, no conflicts fibrochondrogenesis 1 germline unknown Detail
Benign 2024-02-01 criteria provided, single submitter not provided germline Detail
Benign 2021-07-22 criteria provided, single submitter Hearing loss, autosomal dominant 37 germline Detail
Benign 2021-07-22 criteria provided, single submitter Marshall syndrome germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.121 glaucoma Genome-wide association analyses identify three new susceptibility loci for prim... GWASCAT 22922875 Detail
0.001 primary angle-closure glaucoma Three susceptibility loci for primary angle-closure glaucoma (PACG) were recentl... BeFree 23920366 Detail
0.001 primary angle-closure glaucoma Three susceptibility loci for primary angle-closure glaucoma (PACG) were recentl... BeFree 23920366 Detail
0.001 primary angle-closure glaucoma Three susceptibility loci for primary angle-closure glaucoma (PACG) were recentl... BeFree 23920366 Detail
0.001 primary angle-closure glaucoma Recently, three genetic susceptibility loci for primary angle closure glaucoma (... BeFree 24474268 Detail
0.001 primary angle-closure glaucoma Three loci defined by single nucleotide polymorphisms (SNPs) rs11024102 in PLEKH... BeFree 23847314 Detail
0.001 primary angle-closure glaucoma Recently, three genetic susceptibility loci for primary angle closure glaucoma (... BeFree 24474268 Detail
0.001 primary angle-closure glaucoma Three susceptibility loci for primary angle-closure glaucoma (PACG) were recentl... BeFree 23920366 Detail
0.001 primary angle-closure glaucoma Recently, three genetic susceptibility loci for primary angle closure glaucoma (... BeFree 24474268 Detail
0.001 primary angle-closure glaucoma Three loci defined by single nucleotide polymorphisms (SNPs) rs11024102 in PLEKH... BeFree 23847314 Detail
0.001 primary angle-closure glaucoma Recently, three genetic susceptibility loci for primary angle closure glaucoma (... BeFree 24474268 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001854.4(COL11A1):c.3968C>T (p.Pro1323Leu) AND not specified ClinVar Detail
NM_001854.4(COL11A1):c.3968C>T (p.Pro1323Leu) AND Stickler syndrome type 2 ClinVar Detail
NM_001854.4(COL11A1):c.3968C>T (p.Pro1323Leu) AND Fibrochondrogenesis 1 ClinVar Detail
NM_001854.4(COL11A1):c.3968C>T (p.Pro1323Leu) AND not provided ClinVar Detail
NM_001854.4(COL11A1):c.3968C>T (p.Pro1323Leu) AND Hearing loss, autosomal dominant 37 ClinVar Detail
NM_001854.4(COL11A1):c.3968C>T (p.Pro1323Leu) AND Marshall syndrome ClinVar Detail
Genome-wide association analyses identify three new susceptibility loci for primary angle closure gl... DisGeNET Detail
Three susceptibility loci for primary angle-closure glaucoma (PACG) were recently identified: PLEKHA... DisGeNET Detail
Three susceptibility loci for primary angle-closure glaucoma (PACG) were recently identified: PLEKHA... DisGeNET Detail
Three susceptibility loci for primary angle-closure glaucoma (PACG) were recently identified: PLEKHA... DisGeNET Detail
Recently, three genetic susceptibility loci for primary angle closure glaucoma (PACG) were identifie... DisGeNET Detail
Three loci defined by single nucleotide polymorphisms (SNPs) rs11024102 in PLEKHA7, rs3753841 in COL... DisGeNET Detail
Recently, three genetic susceptibility loci for primary angle closure glaucoma (PACG) were identifie... DisGeNET Detail
Three susceptibility loci for primary angle-closure glaucoma (PACG) were recently identified: PLEKHA... DisGeNET Detail
Recently, three genetic susceptibility loci for primary angle closure glaucoma (PACG) were identifie... DisGeNET Detail
Three loci defined by single nucleotide polymorphisms (SNPs) rs11024102 in PLEKHA7, rs3753841 in COL... DisGeNET Detail
Recently, three genetic susceptibility loci for primary angle closure glaucoma (PACG) were identifie... 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
rs3753841 dbSNP
Genome
hg19
Position
chr1:103,379,918-103,379,918
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1142
Mean of sample read depth (HGVD)
44.26
Standard deviation of sample read depth (HGVD)
18.81
Number of reference allele (HGVD)
731
Number of alternative allele (HGVD)
1553
Allele Frequency (HGVD)
0.6799474605954466
Gene Symbol (HGVD)
COL11A1
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))
rs3753841
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6524
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10935
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8620
East Asian Allele Counts (ExAC)
5941
East Asian Heterozygous Counts (ExAC)
1829
East Asian Homozygous Counts (ExAC)
2056
East Asian Allele Frequency (ExAC)
0.6892111368909513
Chromosome Counts in All Race (ExAC)
119810
Allele Counts in All Race (ExAC)
70874
Heterozygous Counts in All Race (ExAC)
26240
Homozygous Counts in All Race (ExAC)
22317
Allele Frequency in All Race (ExAC)
0.591553292713463
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