rs2073575350

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_024034.6(GDAP1L1):​c.347A>C​(p.Asp116Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,592 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 6.8e-7 ( 0 hom. )

Consequence

GDAP1L1
NM_024034.6 missense

Scores

3
11
5

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 8.91
Variant links:
Genes affected
GDAP1L1 (HGNC:4213): (ganglioside induced differentiation associated protein 1 like 1) The ganglioside GD3 synthase causes cell differentiation with neurite sprouting when transfected into the mouse neuroblastoma cell line Neuro2a. After differentiation, the expression of several genes is upregulated, including one that encodes a protein termed ganglioside-induced differentiation-associated protein 1 (Gdap1). A similar gene was found in humans, and mutations in the human gene are associated with Charcot-Marie-Tooth type 4A disease. The protein encoded by this gene is similar in sequence to the human GDAP1 protein. Several transcript variants encoding different isoforms, as well as a noncoding transcript variant, have been found for this gene. [provided by RefSeq, Feb 2012]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GDAP1L1NM_024034.6 linkc.347A>C p.Asp116Ala missense_variant Exon 2 of 6 ENST00000342560.10 NP_076939.3 Q96MZ0-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GDAP1L1ENST00000342560.10 linkc.347A>C p.Asp116Ala missense_variant Exon 2 of 6 1 NM_024034.6 ENSP00000341782.5 Q96MZ0-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461592
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
727100
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:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.41
BayesDel_addAF
Pathogenic
0.25
D
BayesDel_noAF
Uncertain
0.12
CADD
Pathogenic
29
DANN
Uncertain
1.0
DEOGEN2
Benign
0.12
T;T;.;.;.;.
Eigen
Uncertain
0.51
Eigen_PC
Uncertain
0.58
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.95
D;D;D;D;D;D
M_CAP
Benign
0.047
D
MetaRNN
Uncertain
0.63
D;D;D;D;D;D
MetaSVM
Benign
-0.48
T
MutationAssessor
Benign
1.9
.;L;L;.;.;L
PrimateAI
Uncertain
0.78
T
PROVEAN
Uncertain
-3.7
.;D;.;.;D;N
REVEL
Uncertain
0.44
Sift
Uncertain
0.0030
.;D;.;.;T;T
Sift4G
Pathogenic
0.0
D;D;D;D;D;D
Polyphen
1.0
.;D;.;.;.;.
Vest4
0.88
MutPred
0.52
.;Loss of stability (P = 0.1371);Loss of stability (P = 0.1371);Loss of stability (P = 0.1371);Loss of stability (P = 0.1371);Loss of stability (P = 0.1371);
MVP
0.39
MPC
1.5
ClinPred
0.99
D
GERP RS
5.5
Varity_R
0.57
gMVP
0.50

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr20-42885959; API