2-101698111-G-A

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2

The NM_001395002.1(MAP4K4):​c.31G>A​(p.Val11Met) variant causes a missense change. The variant allele was found at a frequency of 0.00000786 in 1,145,166 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000079 ( 0 hom. )

Consequence

MAP4K4
NM_001395002.1 missense

Scores

3
4
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.16
Variant links:
Genes affected
MAP4K4 (HGNC:6866): (mitogen-activated protein kinase kinase kinase kinase 4) The protein encoded by this gene is a member of the serine/threonine protein kinase family. This kinase has been shown to specifically activate MAPK8/JNK. The activation of MAPK8 by this kinase is found to be inhibited by the dominant-negative mutants of MAP3K7/TAK1, MAP2K4/MKK4, and MAP2K7/MKK7, which suggests that this kinase may function through the MAP3K7-MAP2K4-MAP2K7 kinase cascade, and mediate the TNF-alpha signaling pathway. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.27116418).
BS2
High AC in GnomAdExome4 at 9 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MAP4K4NM_001395002.1 linkuse as main transcriptc.31G>A p.Val11Met missense_variant 1/33 ENST00000324219.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MAP4K4ENST00000324219.9 linkuse as main transcriptc.31G>A p.Val11Met missense_variant 1/335 NM_001395002.1 P3

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000786
AC:
9
AN:
1145166
Hom.:
0
Cov.:
30
AF XY:
0.00000704
AC XY:
4
AN XY:
567784
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:
0.00000980
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000378

ClinVar

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

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsMar 01, 2024The c.31G>A (p.V11M) alteration is located in exon 1 (coding exon 1) of the MAP4K4 gene. This alteration results from a G to A substitution at nucleotide position 31, causing the valine (V) at amino acid position 11 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.60
BayesDel_addAF
Benign
-0.070
T
BayesDel_noAF
Benign
-0.34
CADD
Uncertain
24
DANN
Uncertain
0.99
DEOGEN2
Benign
0.015
T;.;T;T;.;.;T;T;.;T;.
Eigen
Benign
-0.079
Eigen_PC
Benign
-0.078
FATHMM_MKL
Uncertain
0.84
D
LIST_S2
Uncertain
0.97
D;D;D;D;D;D;D;D;D;D;D
M_CAP
Pathogenic
0.31
D
MetaRNN
Benign
0.27
T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.61
T
MutationAssessor
Benign
0.34
.;N;.;.;.;N;.;.;.;N;.
MutationTaster
Benign
0.87
D;D;N;N;N;N;N
PrimateAI
Pathogenic
0.83
D
PROVEAN
Benign
-0.66
N;.;N;N;N;.;N;.;.;N;N
REVEL
Benign
0.21
Sift
Benign
0.039
D;.;D;D;D;.;D;.;.;D;D
Sift4G
Uncertain
0.057
T;D;D;D;D;T;D;D;D;D;D
Polyphen
0.52, 0.99, 0.39
.;.;P;D;B;D;.;.;.;B;.
Vest4
0.18, 0.17, 0.19, 0.18, 0.35, 0.38, 0.34, 0.27, 0.30
MutPred
0.33
Gain of disorder (P = 0.0551);Gain of disorder (P = 0.0551);Gain of disorder (P = 0.0551);Gain of disorder (P = 0.0551);Gain of disorder (P = 0.0551);Gain of disorder (P = 0.0551);Gain of disorder (P = 0.0551);Gain of disorder (P = 0.0551);Gain of disorder (P = 0.0551);Gain of disorder (P = 0.0551);Gain of disorder (P = 0.0551);
MVP
0.54
MPC
1.5
ClinPred
0.68
D
GERP RS
2.2
RBP_binding_hub_radar
1.1
RBP_regulation_power_radar
2.8
Varity_R
0.34
gMVP
0.68

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: rs2035271150; hg19: chr2-102314573; API