NM_001010904.2:c.599C>T

Variant summary

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

The NM_001010904.2(GLYATL3):​c.599C>T​(p.Pro200Leu) 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 pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P200Q) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

GLYATL3
NM_001010904.2 missense

Scores

3
5
11

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.95
Variant links:
Genes affected
GLYATL3 (HGNC:21349): (glycine-N-acyltransferase like 3) Predicted to enable glycine N-acyltransferase activity. Predicted to be located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

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, 0.904

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GLYATL3NM_001010904.2 linkc.599C>T p.Pro200Leu missense_variant Exon 6 of 6 ENST00000371197.9 NP_001010904.1 Q5SZD4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GLYATL3ENST00000371197.9 linkc.599C>T p.Pro200Leu missense_variant Exon 6 of 6 2 NM_001010904.2 ENSP00000360240.4 Q5SZD4
GLYATL3ENST00000545705.1 linkc.*131C>T downstream_gene_variant 5 ENSP00000440029.1 F5GXQ5

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.0000282
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.16
BayesDel_addAF
Uncertain
0.077
D
BayesDel_noAF
Benign
-0.13
CADD
Benign
23
DANN
Uncertain
0.98
DEOGEN2
Benign
0.18
T
Eigen
Uncertain
0.27
Eigen_PC
Uncertain
0.29
FATHMM_MKL
Benign
0.66
D
LIST_S2
Benign
0.69
T
M_CAP
Benign
0.019
T
MetaRNN
Pathogenic
0.90
D
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.30
N
PrimateAI
Benign
0.44
T
PROVEAN
Pathogenic
-7.9
D
REVEL
Uncertain
0.36
Sift
Benign
0.13
T
Sift4G
Pathogenic
0.0
D
Polyphen
1.0
D
Vest4
0.55
MutPred
0.77
Gain of sheet (P = 0.039);
MVP
0.12
ClinPred
0.97
D
GERP RS
6.1
Varity_R
0.42
gMVP
0.86

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: rs1389168434; hg19: chr6-49494359; API