21-46266025-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The NM_003906.5(MCM3AP):​c.2931T>A​(p.His977Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,244 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. H977H) has been classified as Benign.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

MCM3AP
NM_003906.5 missense

Scores

5
3
11

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.256
Variant links:
Genes affected
MCM3AP (HGNC:6946): (minichromosome maintenance complex component 3 associated protein) The minichromosome maintenance protein 3 (MCM3) is one of the MCM proteins essential for the initiation of DNA replication. The protein encoded by this gene is a MCM3 binding protein. It was reported to have phosphorylation-dependent DNA-primase activity, which was up-regulated in antigen immunization induced germinal center. This protein was demonstrated to be an acetyltransferase that acetylates MCM3 and plays a role in DNA replication. The mutagenesis of a nuclear localization signal of MCM3 affects the binding of this protein with MCM3, suggesting that this protein may also facilitate MCM3 nuclear localization. This gene is expressed in the brain or in neuronal tissue. An allelic variant encoding amino acid Lys at 915, instead of conserved Glu, has been identified in patients with mild intellectual disability. [provided by RefSeq, Jan 2014]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.751

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MCM3APNM_003906.5 linkc.2931T>A p.His977Gln missense_variant Exon 11 of 28 ENST00000291688.6 NP_003897.2 O60318-1
MCM3APXM_005261203.5 linkc.2931T>A p.His977Gln missense_variant Exon 12 of 29 XP_005261260.1 O60318-1
MCM3APXM_005261204.6 linkc.2931T>A p.His977Gln missense_variant Exon 12 of 29 XP_005261261.1 O60318-1
MCM3APXM_005261205.5 linkc.2931T>A p.His977Gln missense_variant Exon 12 of 29 XP_005261262.1 O60318-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MCM3APENST00000291688.6 linkc.2931T>A p.His977Gln missense_variant Exon 11 of 28 1 NM_003906.5 ENSP00000291688.1 O60318-1
MCM3APENST00000397708.1 linkc.2931T>A p.His977Gln missense_variant Exon 12 of 29 5 ENSP00000380820.1 O60318-1
MCM3APENST00000486937.5 linkn.1223T>A non_coding_transcript_exon_variant Exon 2 of 18 2
MCM3APENST00000496607.5 linkn.928T>A non_coding_transcript_exon_variant Exon 1 of 18 2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.85e-7
AC:
1
AN:
1459244
Hom.:
0
Cov.:
46
AF XY:
0.00
AC XY:
0
AN XY:
725696
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:
9.00e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.64
BayesDel_addAF
Benign
-0.031
T
BayesDel_noAF
Benign
-0.28
CADD
Benign
12
DANN
Benign
0.90
DEOGEN2
Uncertain
0.67
D;D
Eigen
Benign
-0.58
Eigen_PC
Benign
-0.81
FATHMM_MKL
Benign
0.21
N
LIST_S2
Benign
0.85
D;.
M_CAP
Benign
0.017
T
MetaRNN
Pathogenic
0.75
D;D
MetaSVM
Benign
-1.2
T
MutationAssessor
Uncertain
2.4
M;M
PrimateAI
Uncertain
0.56
T
PROVEAN
Pathogenic
-6.5
D;D
REVEL
Benign
0.29
Sift
Pathogenic
0.0
D;D
Sift4G
Pathogenic
0.0
D;D
Polyphen
0.96
D;D
Vest4
0.40
MutPred
0.28
Gain of solvent accessibility (P = 0.0081);Gain of solvent accessibility (P = 0.0081);
MVP
0.39
MPC
0.57
ClinPred
0.92
D
GERP RS
-0.97
Varity_R
0.62
gMVP
0.63

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr21-47685939; API