1-11965591-G-A

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1

The NM_000302.4(PLOD1):​c.1582G>A​(p.Glu528Lys) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000173 in 1,598,152 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.00077 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00011 ( 0 hom. )

Consequence

PLOD1
NM_000302.4 missense, splice_region

Scores

8
11
Splicing: ADA: 0.0001462
2

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:3B:3

Conservation

PhyloP100: 4.63
Variant links:
Genes affected
PLOD1 (HGNC:9081): (procollagen-lysine,2-oxoglutarate 5-dioxygenase 1) Lysyl hydroxylase is a membrane-bound homodimeric protein localized to the cisternae of the endoplasmic reticulum. The enzyme (cofactors iron and ascorbate) catalyzes the hydroxylation of lysyl residues in collagen-like peptides. The resultant hydroxylysyl groups are attachment sites for carbohydrates in collagen and thus are critical for the stability of intermolecular crosslinks. Some patients with Ehlers-Danlos syndrome type VI have deficiencies in lysyl hydroxylase activity. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.016842455).
BP6
Variant 1-11965591-G-A is Benign according to our data. Variant chr1-11965591-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 459811.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=3, Likely_benign=3}.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000775 (118/152304) while in subpopulation AFR AF= 0.00262 (109/41558). AF 95% confidence interval is 0.00222. There are 0 homozygotes in gnomad4. There are 51 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PLOD1NM_000302.4 linkc.1582G>A p.Glu528Lys missense_variant, splice_region_variant Exon 14 of 19 ENST00000196061.5 NP_000293.2 Q02809-1
PLOD1NM_001316320.2 linkc.1723G>A p.Glu575Lys missense_variant, splice_region_variant Exon 15 of 20 NP_001303249.1 Q02809-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PLOD1ENST00000196061.5 linkc.1582G>A p.Glu528Lys missense_variant, splice_region_variant Exon 14 of 19 1 NM_000302.4 ENSP00000196061.4 Q02809-1
PLOD1ENST00000470133.1 linkn.196G>A splice_region_variant, non_coding_transcript_exon_variant Exon 2 of 3 3
PLOD1ENST00000491536.5 linkn.210G>A splice_region_variant, non_coding_transcript_exon_variant Exon 2 of 5 3

Frequencies

GnomAD3 genomes
AF:
0.000775
AC:
118
AN:
152186
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00263
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000458
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:
0.0000294
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000295
AC:
74
AN:
250438
Hom.:
0
AF XY:
0.000251
AC XY:
34
AN XY:
135528
show subpopulations
Gnomad AFR exome
AF:
0.00333
Gnomad AMR exome
AF:
0.0000579
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000163
Gnomad FIN exome
AF:
0.0000464
Gnomad NFE exome
AF:
0.0000974
Gnomad OTH exome
AF:
0.000163
GnomAD4 exome
AF:
0.000109
AC:
158
AN:
1445848
Hom.:
0
Cov.:
28
AF XY:
0.000101
AC XY:
73
AN XY:
720288
show subpopulations
Gnomad4 AFR exome
AF:
0.00304
Gnomad4 AMR exome
AF:
0.0000895
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.000128
Gnomad4 FIN exome
AF:
0.0000189
Gnomad4 NFE exome
AF:
0.0000200
Gnomad4 OTH exome
AF:
0.000284
GnomAD4 genome
AF:
0.000775
AC:
118
AN:
152304
Hom.:
0
Cov.:
31
AF XY:
0.000685
AC XY:
51
AN XY:
74474
show subpopulations
Gnomad4 AFR
AF:
0.00262
Gnomad4 AMR
AF:
0.000458
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000185
Hom.:
0
Bravo
AF:
0.00108
ESP6500AA
AF:
0.00250
AC:
11
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.000412
AC:
50
Asia WGS
AF:
0.000577
AC:
2
AN:
3478
EpiCase
AF:
0.00
EpiControl
AF:
0.0000593

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:3Benign:3
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitterclinical testingMayo Clinic Laboratories, Mayo ClinicOct 18, 2022BS1 -
Likely benign, criteria provided, single submitterclinical testingGeneDxMay 12, 2020- -
Ehlers-Danlos syndrome, kyphoscoliotic type 1 Uncertain:1Benign:1
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 27, 2025- -
Uncertain significance, criteria provided, single submitterclinical testingARUP Laboratories, Molecular Genetics and Genomics, ARUP LaboratoriesApr 29, 2021The PLOD1 c.1582G>A; p.Glu528Lys variant (rs112250644), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 459811). This variant is found in the African/African-American population with an allele frequency of 0.27% (68/24928 alleles) in the Genome Aggregation Database. The glutamate at codon 528 is moderately conserved, and computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.537). Due to limited information, the clinical significance of the p.Glu528Lys variant is uncertain at this time. -
not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpSep 03, 2024- -
Familial thoracic aortic aneurysm and aortic dissection Benign:1
Likely benign, criteria provided, single submitterclinical testingAmbry GeneticsJul 10, 2017This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.089
BayesDel_addAF
Benign
-0.16
T
BayesDel_noAF
Uncertain
-0.010
CADD
Uncertain
24
DANN
Uncertain
0.99
DEOGEN2
Benign
0.041
T
Eigen
Benign
-0.089
Eigen_PC
Benign
-0.031
FATHMM_MKL
Uncertain
0.97
D
LIST_S2
Uncertain
0.92
D
M_CAP
Uncertain
0.098
D
MetaRNN
Benign
0.017
T
MetaSVM
Uncertain
-0.21
T
MutationAssessor
Benign
1.5
L
PrimateAI
Uncertain
0.58
T
PROVEAN
Benign
-0.50
N
REVEL
Uncertain
0.54
Sift
Benign
0.29
T
Sift4G
Benign
0.29
T
Polyphen
0.63
P
Vest4
0.69
MVP
0.89
MPC
0.23
ClinPred
0.012
T
GERP RS
4.6
Varity_R
0.10
gMVP
0.70

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.00015
dbscSNV1_RF
Benign
0.0020
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

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

Other links and lift over

dbSNP: rs112250644; hg19: chr1-12025648; COSMIC: COSV105054981; API