11-63636274-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_015459.5(ATL3):​c.911C>G​(p.Ser304Cys) 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. 13/21 in silico tools predict a benign 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

ATL3
NM_015459.5 missense

Scores

5
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.760
Variant links:
Genes affected
ATL3 (HGNC:24526): (atlastin GTPase 3) This gene encodes a member of a family of dynamin-like, integral membrane GTPases. The encoded protein is required for the proper formation of the network of interconnected tubules of the endoplasmic reticulum. Mutations in this gene may be associated with hereditary sensory neuropathy type IF. Alternatively spliced transcript variants that encode distinct isoforms have been described. [provided by RefSeq, Feb 2014]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.17068097).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ATL3NM_015459.5 linkuse as main transcriptc.911C>G p.Ser304Cys missense_variant 9/13 ENST00000398868.8 NP_056274.3 Q6DD88
ATL3NM_001290048.2 linkuse as main transcriptc.857C>G p.Ser286Cys missense_variant 9/13 NP_001276977.1 Q6DD88F5H6I7B4DXC4
ATL3XM_047426725.1 linkuse as main transcriptc.1067C>G p.Ser356Cys missense_variant 10/14 XP_047282681.1
ATL3XM_006718493.2 linkuse as main transcriptc.854C>G p.Ser285Cys missense_variant 8/12 XP_006718556.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ATL3ENST00000398868.8 linkuse as main transcriptc.911C>G p.Ser304Cys missense_variant 9/131 NM_015459.5 ENSP00000381844.3 Q6DD88
ATL3ENST00000538786.1 linkuse as main transcriptc.857C>G p.Ser286Cys missense_variant 9/132 ENSP00000437593.1 F5H6I7

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
30
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.089
BayesDel_addAF
Benign
-0.066
T
BayesDel_noAF
Benign
-0.33
CADD
Uncertain
25
DANN
Uncertain
0.99
DEOGEN2
Uncertain
0.58
D;.
Eigen
Benign
-0.15
Eigen_PC
Benign
-0.059
FATHMM_MKL
Benign
0.26
N
LIST_S2
Benign
0.69
T;T
M_CAP
Benign
0.033
D
MetaRNN
Benign
0.17
T;T
MetaSVM
Benign
-0.62
T
MutationAssessor
Benign
1.9
L;.
PrimateAI
Benign
0.31
T
PROVEAN
Uncertain
-3.5
D;D
REVEL
Benign
0.24
Sift
Uncertain
0.0020
D;D
Sift4G
Uncertain
0.010
D;D
Polyphen
0.15
B;.
Vest4
0.21
MutPred
0.37
Loss of disorder (P = 0.0088);.;
MVP
0.82
MPC
0.66
ClinPred
0.93
D
GERP RS
3.6
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.48
gMVP
0.14

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs757344746; hg19: chr11-63403746; API