chr17-45264701-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP2PP3

The NM_003954.5(MAP3K14):​c.2779G>A​(p.Ala927Thr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

MAP3K14
NM_003954.5 missense

Scores

7
7
1

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.82
Variant links:
Genes affected
MAP3K14 (HGNC:6853): (mitogen-activated protein kinase kinase kinase 14) This gene encodes mitogen-activated protein kinase kinase kinase 14, which is a serine/threonine protein-kinase. This kinase binds to TRAF2 and stimulates NF-kappaB activity. It shares sequence similarity with several other MAPKK kinases. It participates in an NF-kappaB-inducing signalling cascade common to receptors of the tumour-necrosis/nerve-growth factor (TNF/NGF) family and to the interleukin-1 type-I receptor. [provided by RefSeq, Jul 2008]
MAP3K14-AS1 (HGNC:44359): (MAP3K14 antisense RNA 1)

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP2
Missense variant in gene, where missense usually causes diseases (based on misZ statistic), MAP3K14. . Trascript score misZ 4.5031 (greater than threshold 3.09). GenCC has associacion of gene with NIK deficiency.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.789

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MAP3K14NM_003954.5 linkuse as main transcriptc.2779G>A p.Ala927Thr missense_variant 16/16 ENST00000344686.8
MAP3K14-AS1NR_110325.1 linkuse as main transcriptn.260-2412C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MAP3K14ENST00000344686.8 linkuse as main transcriptc.2779G>A p.Ala927Thr missense_variant 16/161 NM_003954.5 P1
MAP3K14-AS1ENST00000657572.1 linkuse as main transcriptn.170-2412C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

NIK deficiency Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingInvitaeJul 05, 2018This sequence change replaces alanine with threonine at codon 927 of the MAP3K14 protein (p.Ala927Thr). The alanine residue is highly conserved and there is a small physicochemical difference between alanine and threonine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with MAP3K14-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.85
BayesDel_addAF
Uncertain
0.16
D
BayesDel_noAF
Uncertain
-0.010
CADD
Pathogenic
26
DANN
Pathogenic
1.0
DEOGEN2
Uncertain
0.46
T;T;T
Eigen
Pathogenic
0.75
Eigen_PC
Pathogenic
0.74
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Benign
0.85
.;D;.
MetaRNN
Pathogenic
0.79
D;D;D
MetaSVM
Uncertain
-0.21
T
MutationAssessor
Uncertain
2.1
M;M;M
PrimateAI
Uncertain
0.63
T
REVEL
Uncertain
0.36
Sift4G
Pathogenic
0.0
.;D;D
Polyphen
1.0
D;D;D
Vest4
0.89, 0.89
MutPred
0.36
Gain of phosphorylation at A927 (P = 0.0596);Gain of phosphorylation at A927 (P = 0.0596);Gain of phosphorylation at A927 (P = 0.0596);
MVP
0.34
ClinPred
0.97
D
GERP RS
5.7
Varity_R
0.33
gMVP
0.79

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: rs1567984601; hg19: chr17-43342068; API