NM_001042600.3:c.1453G>T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001042600.3(MAP4K1):c.1453G>T(p.Ala485Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000355 in 1,606,402 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001042600.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAP4K1 | NM_001042600.3 | c.1453G>T | p.Ala485Ser | missense_variant | Exon 20 of 31 | ENST00000396857.7 | NP_001036065.1 | |
MAP4K1 | NM_007181.6 | c.1453G>T | p.Ala485Ser | missense_variant | Exon 20 of 32 | NP_009112.1 | ||
MAP4K1 | XM_011526404.2 | c.1573G>T | p.Ala525Ser | missense_variant | Exon 21 of 32 | XP_011524706.1 | ||
MAP4K1-AS1 | NR_134907.1 | n.340C>A | non_coding_transcript_exon_variant | Exon 3 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000303 AC: 7AN: 230956Hom.: 0 AF XY: 0.0000319 AC XY: 4AN XY: 125390
GnomAD4 exome AF: 0.0000351 AC: 51AN: 1454288Hom.: 0 Cov.: 31 AF XY: 0.0000387 AC XY: 28AN XY: 722584
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1453G>T (p.A485S) alteration is located in exon 20 (coding exon 20) of the MAP4K1 gene. This alteration results from a G to T substitution at nucleotide position 1453, causing the alanine (A) at amino acid position 485 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at