chr1-231241424-ACCAGTC-A

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4

The NM_014236.4(GNPAT):​c.51_56del​(p.Pro18_Ser19del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

GNPAT
NM_014236.4 inframe_deletion

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.28
Variant links:
Genes affected
GNPAT (HGNC:4416): (glyceronephosphate O-acyltransferase) This gene encodes an enzyme located in the peroxisomal membrane which is essential to the synthesis of ether phospholipids. Mutations in this gene are associated with rhizomelic chondrodysplasia punctata. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_014236.4.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GNPATNM_014236.4 linkuse as main transcriptc.51_56del p.Pro18_Ser19del inframe_deletion 1/16 ENST00000366647.9
GNPATNM_001316350.2 linkuse as main transcriptc.51_56del p.Pro18_Ser19del inframe_deletion 1/15
GNPATXM_005273313.5 linkuse as main transcriptc.51_56del p.Pro18_Ser19del inframe_deletion 1/16

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GNPATENST00000366647.9 linkuse as main transcriptc.51_56del p.Pro18_Ser19del inframe_deletion 1/161 NM_014236.4 P1O15228-1
GNPATENST00000416000.1 linkuse as main transcriptc.51_56del p.Pro18_Ser19del inframe_deletion 1/135
GNPATENST00000436239.5 linkuse as main transcriptc.51_56del p.Pro18_Ser19del inframe_deletion 1/63
GNPATENST00000644483.1 linkuse as main transcriptc.51_56del p.Pro18_Ser19del inframe_deletion, NMD_transcript_variant 1/17

Frequencies

GnomAD3 genomes
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingInvitaeJan 02, 2021In 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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals with GNPAT-related conditions. This variant is not present in population databases (ExAC no frequency). This variant, c.51_56del, results in the deletion of 2 amino acid(s) of the GNPAT protein (p.Pro18_Ser19del), but otherwise preserves the integrity of the reading frame. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-231377170; API