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GeneBe

rs30187

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PM2_Supporting

The NM_001040458.3(ERAP1):c.1583A>T(p.Lys528Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K528R) has been classified as Benign.

Frequency

Genomes: not found (cov: 32)

Consequence

ERAP1
NM_001040458.3 missense

Scores

2
7
9

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.43

Links

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 32.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ERAP1NM_001040458.3 linkuse as main transcriptc.1583A>T p.Lys528Met missense_variant 11/19 ENST00000443439.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ERAP1ENST00000443439.7 linkuse as main transcriptc.1583A>T p.Lys528Met missense_variant 11/191 NM_001040458.3 P1Q9NZ08-1
ERAP1ENST00000296754.7 linkuse as main transcriptc.1583A>T p.Lys528Met missense_variant 11/201 Q9NZ08-2
ERAP1ENST00000507859.1 linkuse as main transcriptn.246A>T non_coding_transcript_exon_variant 3/52

Frequencies

GnomAD3 genomes
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.22
BayesDel_addAF
Uncertain
0.030
T
BayesDel_noAF
Benign
-0.19
Cadd
Pathogenic
29
Dann
Uncertain
1.0
Eigen
Uncertain
0.62
Eigen_PC
Pathogenic
0.68
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.87
D;D
M_CAP
Benign
0.019
T
MetaRNN
Uncertain
0.54
D;D
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.3
L;L
MutationTaster
Benign
1.0
D;D;D
PrimateAI
Uncertain
0.61
T
PROVEAN
Uncertain
-2.9
D;D
REVEL
Benign
0.26
Sift
Benign
0.10
T;T
Sift4G
Benign
0.22
T;T
Polyphen
1.0
D;D
Vest4
0.58
MutPred
0.43
Loss of methylation at K528 (P = 0.0073);Loss of methylation at K528 (P = 0.0073);
MVP
0.29
MPC
0.48
ClinPred
0.98
D
GERP RS
6.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.60
gMVP
0.75

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

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

Other links and lift over

dbSNP: rs30187; hg19: chr5-96124330; API