11-106077721-C-T

Variant summary

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

The NM_015423.3(AASDHPPT):​c.11C>T​(p.Pro4Leu) 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. 14/20 in silico tools predict a benign 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. P4R) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Consequence

AASDHPPT
NM_015423.3 missense

Scores

1
18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.109
Variant links:
Genes affected
AASDHPPT (HGNC:14235): (aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase) The protein encoded by this gene is similar to Saccharomyces cerevisiae LYS5, which is required for the activation of the alpha-aminoadipate dehydrogenase in the biosynthetic pathway of lysine. Yeast alpha-aminoadipate dehydrogenase converts alpha-biosynthetic-aminoadipate semialdehyde to alpha-aminoadipate. It has been suggested that defects in the human gene result in pipecolic acidemia. [provided by RefSeq, Jul 2008]

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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=0.091575295).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
AASDHPPTNM_015423.3 linkc.11C>T p.Pro4Leu missense_variant Exon 1 of 6 ENST00000278618.9 NP_056238.2 Q9NRN7-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
AASDHPPTENST00000278618.9 linkc.11C>T p.Pro4Leu missense_variant Exon 1 of 6 1 NM_015423.3 ENSP00000278618.4 Q9NRN7-1
AASDHPPTENST00000524411.5 linkc.-13+1433C>T intron_variant Intron 1 of 4 3 ENSP00000435099.1 E9PLW6
AASDHPPTENST00000533423.5 linkc.-12-1746C>T intron_variant Intron 1 of 3 3 ENSP00000437175.1 E9PNF3
AASDHPPTENST00000525660.1 linkn.11C>T non_coding_transcript_exon_variant Exon 1 of 5 2 ENSP00000437144.1 Q9NRN7-2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Benign
-0.16
T
BayesDel_noAF
Benign
-0.47
CADD
Benign
16
DANN
Benign
0.94
DEOGEN2
Benign
0.11
T
Eigen
Benign
-0.78
Eigen_PC
Benign
-0.80
FATHMM_MKL
Benign
0.075
N
LIST_S2
Benign
0.64
T
M_CAP
Benign
0.041
D
MetaRNN
Benign
0.092
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.4
L
PrimateAI
Uncertain
0.59
T
PROVEAN
Benign
-0.65
N
REVEL
Benign
0.038
Sift
Benign
0.19
T
Sift4G
Benign
0.38
T
Polyphen
0.0
B
Vest4
0.19
MutPred
0.41
Gain of sheet (P = 0.0085);
MVP
0.45
MPC
0.34
ClinPred
0.20
T
GERP RS
2.6
Varity_R
0.042
gMVP
0.59

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: rs1414782237; hg19: chr11-105948448; API