4-87656493-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PVS1_SupportingPM2BS1_Supporting
The NM_004407.4(DMP1):āc.1A>Gā(p.Met1?) variant causes a start lost change. The variant allele was found at a frequency of 0.00000344 in 1,453,326 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004407.4 start_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DMP1 | NM_004407.4 | c.1A>G | p.Met1? | start_lost | Exon 2 of 6 | ENST00000339673.11 | NP_004398.1 | |
DMP1 | NM_001079911.3 | c.1A>G | p.Met1? | start_lost | Exon 2 of 5 | NP_001073380.1 | ||
DMP1 | XM_011531705.3 | c.88A>G | p.Met30Val | missense_variant | Exon 2 of 6 | XP_011530007.1 | ||
DMP1 | XM_011531706.3 | c.88A>G | p.Met30Val | missense_variant | Exon 2 of 5 | XP_011530008.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251412Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135878
GnomAD4 exome AF: 0.00000344 AC: 5AN: 1453326Hom.: 0 Cov.: 29 AF XY: 0.00000553 AC XY: 4AN XY: 723776
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Hypophosphatemic rickets, autosomal recessive, 1 Pathogenic:2
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Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with hypophosphatemic rickets (MIM#241520). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0206 - Variant is predicted to result in a loss of the canonical translation initiation codon (ATG). (SP) 0252 - This variant is homozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (3 heterozygotes, 0 homozygotes). (SP) 0311 - An alternative nucleotide change at the initiation codon is present in gnomAD (v2) (1 heterozygote, 0 homozygotes). (I) 0703 - Other start loss variants comparable to the one identified in this case have moderate previous evidence for pathogenicity. c.2T>A(p.Met1Lys) has been reported once as pathogenic (ClinVar) and c.1A>T(p.Met1Leu) has been reported once in a compound heterozygous individual with autosomal recessive hypophosphatemic rickets (PMID: 36334264). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported once as pathogenic in ClinVar. It has also been reported in nine individuals with hypophosphatemic rickets from five unrelated families in the literature (PMIDs: 17033625, 17033621, 25180662, 23038738). (SP) 0901 - This variant has strong evidence for segregation with disease. This variant has been shown to segregate with disease in a large family (PMID: 17033625). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
not provided Pathogenic:1
Initiation codon variant in a gene for which loss of function is a known mechanism of disease (PMID: 17033621); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25180662, 17033625, 18094488, 19007919, 17033621, 25044680) -
not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at