rs121908113

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PM5PP3_Moderate

The ENST00000220822.12(GDAP1):​c.652C>G​(p.Gln218Glu) 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. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q218P) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 29)

Consequence

GDAP1
ENST00000220822.12 missense

Scores

4
7
8

Clinical Significance

Conflicting classifications of pathogenicity no assertion criteria provided P:1U:1

Conservation

PhyloP100: 7.53
Variant links:
Genes affected
GDAP1 (HGNC:15968): (ganglioside induced differentiation associated protein 1) This gene encodes a member of the ganglioside-induced differentiation-associated protein family, which may play a role in a signal transduction pathway during neuronal development. Mutations in this gene have been associated with various forms of Charcot-Marie-Tooth Disease and neuropathy. Two transcript variants encoding different isoforms and a noncoding variant have been identified for this gene. [provided by RefSeq, Feb 2012]

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ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 8 ACMG points.

PM1
In a domain GST C-terminal (size 156) in uniprot entity GDAP1_HUMAN there are 54 pathogenic changes around while only 0 benign (100%) in ENST00000220822.12
PM2
Very rare variant in population databases, with high coverage;
PM5
Other missense variant is known to change same aminoacid residue: Variant chr8-74363012-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 467767.Status of the report is criteria_provided_single_submitter, 1 stars.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.907

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GDAP1NM_018972.4 linkuse as main transcriptc.652C>G p.Gln218Glu missense_variant 5/6 ENST00000220822.12 NP_061845.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GDAP1ENST00000220822.12 linkuse as main transcriptc.652C>G p.Gln218Glu missense_variant 5/61 NM_018972.4 ENSP00000220822 P3Q8TB36-1

Frequencies

GnomAD3 genomes
Cov.:
29
GnomAD4 exome
Cov.:
27
GnomAD4 genome
Cov.:
29

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Uncertain:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Charcot-Marie-Tooth disease axonal type 2K Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMJan 01, 2008- -
Charcot-Marie-Tooth disease type 4A Uncertain:1
Uncertain significance, no assertion criteria providedliterature onlyInherited Neuropathy Consortium Ii, University Of MiamiJan 06, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.17
BayesDel_addAF
Pathogenic
0.46
D
BayesDel_noAF
Pathogenic
0.43
CADD
Benign
22
DANN
Uncertain
0.98
DEOGEN2
Benign
0.22
T;.
Eigen
Benign
-0.046
Eigen_PC
Benign
0.13
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.93
D;D
M_CAP
Uncertain
0.10
D
MetaRNN
Pathogenic
0.91
D;D
MetaSVM
Uncertain
0.49
D
MutationAssessor
Benign
0.46
N;.
MutationTaster
Benign
1.0
A;A
PrimateAI
Uncertain
0.66
T
PROVEAN
Benign
0.080
N;N
REVEL
Uncertain
0.64
Sift
Benign
0.22
T;T
Sift4G
Uncertain
0.050
T;T
Polyphen
0.25
B;.
Vest4
0.92
MutPred
0.81
Loss of ubiquitination at K214 (P = 0.1278);.;
MVP
0.96
MPC
1.2
ClinPred
0.80
D
GERP RS
4.5
Varity_R
0.30
gMVP
0.67

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: rs121908113; hg19: chr8-75275246; API