16-79598961-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate

The NM_005360.5(MAF):​c.942C>A​(p.His314Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 30)

Consequence

MAF
NM_005360.5 missense

Scores

11
6
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.80
Variant links:
Genes affected
MAF (HGNC:6776): (MAF bZIP transcription factor) The protein encoded by this gene is a DNA-binding, leucine zipper-containing transcription factor that acts as a homodimer or as a heterodimer. Depending on the binding site and binding partner, the encoded protein can be a transcriptional activator or repressor. This protein plays a role in the regulation of several cellular processes, including embryonic lens fiber cell development, increased T-cell susceptibility to apoptosis, and chondrocyte terminal differentiation. Defects in this gene are a cause of juvenile-onset pulverulent cataract as well as congenital cerulean cataract 4 (CCA4). Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2010]

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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;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.894

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAFNM_005360.5 linkc.942C>A p.His314Gln missense_variant Exon 1 of 2 ENST00000326043.5 NP_005351.2 O75444-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAFENST00000326043.5 linkc.942C>A p.His314Gln missense_variant Exon 1 of 2 1 NM_005360.5 ENSP00000327048.4 O75444-1
MAFENST00000569649.1 linkc.942C>A p.His314Gln missense_variant Exon 1 of 2 5 ENSP00000455097.1 H3BP11
MAFENST00000393350.1 linkc.942C>A p.His314Gln missense_variant Exon 1 of 1 6 ENSP00000377019.1 O75444-2

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
Cov.:
37
GnomAD4 genome
Cov.:
30
Bravo
AF:
0.0000113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.97
BayesDel_addAF
Pathogenic
0.18
D
BayesDel_noAF
Uncertain
0.020
CADD
Pathogenic
34
DANN
Uncertain
0.99
DEOGEN2
Pathogenic
0.88
.;.;D
Eigen
Pathogenic
0.72
Eigen_PC
Uncertain
0.66
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.91
D;D;D
M_CAP
Pathogenic
0.61
D
MetaRNN
Pathogenic
0.89
D;D;D
MetaSVM
Pathogenic
0.83
D
MutationAssessor
Uncertain
2.2
.;M;M
PrimateAI
Pathogenic
0.89
D
PROVEAN
Pathogenic
-7.3
D;D;D
REVEL
Pathogenic
0.77
Sift
Benign
0.071
T;T;T
Sift4G
Uncertain
0.0070
D;D;D
Polyphen
1.0
.;D;D
Vest4
0.78
MutPred
0.52
Loss of catalytic residue at L316 (P = 0.0865);Loss of catalytic residue at L316 (P = 0.0865);Loss of catalytic residue at L316 (P = 0.0865);
MVP
0.97
ClinPred
0.99
D
GERP RS
4.0
Varity_R
0.86
gMVP
0.70

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: rs765806184; hg19: chr16-79632858; COSMIC: COSV99077077; COSMIC: COSV99077077; API