14-65077931-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2

The NM_001320415.2(MAX):​c.3G>C​(p.Met1?) variant causes a start lost change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

MAX
NM_001320415.2 start_lost

Scores

7
7
5

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.13
Variant links:
Genes affected
MAX (HGNC:6913): (MYC associated factor X) The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Mutations of this gene have been reported to be associated with hereditary pheochromocytoma. A pseudogene of this gene is located on the long arm of chromosome 7. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PVS1
Start lost variant, next in-frame start position is after 2 pathogenic variants. Next in-frame start position is after 28 codons. Genomic position: 65077368. Lost 0.279 part of the original CDS.
PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAXNM_002382.5 linkc.277G>C p.Ala93Pro missense_variant Exon 4 of 5 ENST00000358664.9 NP_002373.3 P61244-1Q8TAX8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAXENST00000358664.9 linkc.277G>C p.Ala93Pro missense_variant Exon 4 of 5 1 NM_002382.5 ENSP00000351490.4 P61244-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32

ClinVar

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

Submissions by phenotype

Hereditary pheochromocytoma-paraganglioma Uncertain:1
Mar 07, 2017
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

In summary, this variant is a novel missense change with uncertain impact on protein function. It has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a MAX-related disease. This sequence change replaces alanine with proline at codon 93 of the MAX protein (p.Ala93Pro). The alanine residue is highly conserved and there is a small physicochemical difference between alanine and proline. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
1.0
BayesDel_addAF
Pathogenic
0.37
D
BayesDel_noAF
Pathogenic
0.29
CADD
Pathogenic
31
DANN
Benign
0.96
DEOGEN2
Benign
0.37
.;.;.;.;T;T;.;T;.;T
Eigen
Uncertain
0.38
Eigen_PC
Uncertain
0.44
FATHMM_MKL
Pathogenic
1.0
D
LIST_S2
Uncertain
0.96
D;.;D;D;D;D;.;D;D;D
M_CAP
Pathogenic
0.67
D
MetaRNN
Uncertain
0.72
D;D;D;D;D;D;D;D;D;D
MetaSVM
Uncertain
0.15
D
MutationAssessor
Uncertain
2.6
.;M;M;M;.;.;M;.;.;.
PrimateAI
Pathogenic
0.90
D
PROVEAN
Uncertain
-2.4
N;.;N;N;D;D;D;N;N;N
REVEL
Pathogenic
0.80
Sift
Benign
0.13
T;.;T;T;T;T;T;T;T;T
Sift4G
Benign
0.23
T;T;T;T;T;.;T;T;T;T
Polyphen
0.96
D;P;.;D;.;.;P;P;.;.
Vest4
0.72
MutPred
0.41
.;Loss of MoRF binding (P = 0.0716);Loss of MoRF binding (P = 0.0716);Loss of MoRF binding (P = 0.0716);.;.;Loss of MoRF binding (P = 0.0716);.;.;.;
MVP
0.84
MPC
2.0
ClinPred
0.90
D
GERP RS
5.0
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.87
gMVP
0.96

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: rs1555340540; hg19: chr14-65544649; API