10-30313622-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018109.4(MTPAP):c.1736G>A(p.Ser579Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000138 in 1,614,176 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018109.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTPAP | NM_018109.4 | c.1736G>A | p.Ser579Asn | missense_variant | 9/9 | ENST00000263063.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTPAP | ENST00000263063.9 | c.1736G>A | p.Ser579Asn | missense_variant | 9/9 | 1 | NM_018109.4 | P1 | |
MTPAP | ENST00000488290.5 | n.3491G>A | non_coding_transcript_exon_variant | 17/17 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000346 AC: 87AN: 251368Hom.: 0 AF XY: 0.000287 AC XY: 39AN XY: 135868
GnomAD4 exome AF: 0.000140 AC: 204AN: 1461846Hom.: 0 Cov.: 31 AF XY: 0.000118 AC XY: 86AN XY: 727222
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152330Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74484
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Nov 01, 2022 | This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 579 of the MTPAP protein (p.Ser579Asn). This variant is present in population databases (rs148562969, gnomAD 0.4%). This missense change has been observed in individual(s) with MTPAP-related conditions (PMID: 32369273). ClinVar contains an entry for this variant (Variation ID: 1429438). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The asparagine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at