rs712701
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_001366110.1(PAX4):āc.986A>Cā(p.His329Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 1,604,714 control chromosomes in the GnomAD database, including 474,935 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001366110.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAX4 | NM_001366110.1 | c.986A>C | p.His329Pro | missense_variant | 12/12 | ENST00000639438.3 | |
PAX4 | NM_001366111.1 | c.914-149A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAX4 | ENST00000639438.3 | c.986A>C | p.His329Pro | missense_variant | 12/12 | 5 | NM_001366110.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.744 AC: 113033AN: 152018Hom.: 42543 Cov.: 33
GnomAD3 exomes AF: 0.735 AC: 173183AN: 235698Hom.: 64830 AF XY: 0.739 AC XY: 94211AN XY: 127402
GnomAD4 exome AF: 0.767 AC: 1114723AN: 1452578Hom.: 432365 Cov.: 65 AF XY: 0.767 AC XY: 553258AN XY: 721650
GnomAD4 genome ? AF: 0.743 AC: 113111AN: 152136Hom.: 42570 Cov.: 33 AF XY: 0.738 AC XY: 54840AN XY: 74358
ClinVar
Submissions by phenotype
Maturity onset diabetes mellitus in young Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | research | Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic | - | Though PAX4 gene is associated with MODY, no sufficeint evidence is found to ascertain the role of this particular variant rs712701 in MODY yet. More clinical studies are required to validate the association. - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 27, 2013 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | This variant is associated with the following publications: (PMID: 15509590, 20360641, 15834548, 27334367) - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Type 2 diabetes mellitus Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at