Menu
GeneBe

6-37644563-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_153487.4(MDGA1):c.2335C>T(p.Leu779Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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)

Consequence

MDGA1
NM_153487.4 missense

Scores

7
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.10
Variant links:
Genes affected
MDGA1 (HGNC:19267): (MAM domain containing glycosylphosphatidylinositol anchor 1) This gene encodes a glycosylphosphatidylinositol (GPI)-anchored cell surface glycoprotein that is expressed predominantly in the developing nervous system. In addition to possessing several cell adhesion molecule-like domains, the mature protein has six Ig-like domains, a single fibronectin type III domain, a MAM domain and a C-terminal GPI-anchoring site. Studies in other mammals suggest this protein plays a role in cell adhesion, migration, and axon guidance and, in the developing brain, neuronal migration. In humans, this gene is associated with bipolar disorder and schizophrenia. [provided by RefSeq, Oct 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2965386).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MDGA1NM_153487.4 linkuse as main transcriptc.2335C>T p.Leu779Phe missense_variant 13/17 ENST00000434837.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MDGA1ENST00000434837.8 linkuse as main transcriptc.2335C>T p.Leu779Phe missense_variant 13/171 NM_153487.4 P1Q8NFP4-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingGenomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of PhiladelphiaJul 15, 2015- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.11
T
BayesDel_noAF
Benign
-0.39
Cadd
Pathogenic
28
Dann
Uncertain
1.0
DEOGEN2
Benign
0.064
T;.;.
Eigen
Uncertain
0.58
Eigen_PC
Uncertain
0.58
FATHMM_MKL
Uncertain
0.84
D
LIST_S2
Uncertain
0.89
D;D;D
M_CAP
Benign
0.010
T
MetaRNN
Benign
0.30
T;T;T
MetaSVM
Benign
-0.90
T
MutationAssessor
Uncertain
2.1
M;.;M
MutationTaster
Benign
0.97
D;D;D
PrimateAI
Uncertain
0.72
T
PROVEAN
Benign
-0.97
N;.;N
REVEL
Benign
0.17
Sift
Benign
0.051
T;.;T
Sift4G
Benign
0.26
T;.;T
Polyphen
0.99
D;.;D
Vest4
0.55
MutPred
0.38
Loss of stability (P = 0.1827);Loss of stability (P = 0.1827);Loss of stability (P = 0.1827);
MVP
0.25
MPC
1.0
ClinPred
0.86
D
GERP RS
5.2
Varity_R
0.18
gMVP
0.47

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: rs864309630; hg19: chr6-37612339; API