chr1-160032009-G-C

Variant names:

• chr1-160032009-G-C
• rs587776528
• ENST00000772608.1:n.313G>C

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 3P and 1B. PM2 PP5 BP4

The ENST00000772608.1(ENSG00000300536):​n.313G>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.00000248 in 403,074 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000025 (0 hom.)
• Consequence: ENSG00000300536 ENST00000772608.1 non_coding_transcript_exon
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 3.87
• Publications: 5 publications found

Genes affected

ENSG00000300536 (HGNC:):

KCNJ10 (HGNC:6256): (potassium inwardly rectifying channel subfamily J member 10) This gene encodes a member of the inward rectifier-type potassium channel family, characterized by having a greater tendency to allow potassium to flow into, rather than out of, a cell. The encoded protein may form a heterodimer with another potassium channel protein and may be responsible for the potassium buffering action of glial cells in the brain. Mutations in this gene have been associated with seizure susceptibility of common idiopathic generalized epilepsy syndromes. [provided by RefSeq, Jul 2008]

PIGM (HGNC:18858): (phosphatidylinositol glycan anchor biosynthesis class M) This gene encodes a transmembrane protein that is located in the endoplasmic reticulum and is involved in GPI-anchor biosynthesis. The glycosylphosphatidylinositol (GPI)-anchor is a glycolipid which contains three mannose molecules in its core backbone. The GPI-anchor is found on many blood cells and serves to anchor proteins to the cell surface. This gene encodes a mannosyltransferase, GPI-MT-I, that transfers the first mannose to GPI on the lumenal side of the endoplasmic reticulum. [provided by RefSeq, Jul 2008]

PIGM Gene-Disease associations (from GenCC):

• hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency

  Inheritance: Unknown, AR Classification: MODERATE, SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P, Orphanet, Ambry Genetics, PanelApp Australia

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 1-160032009-G-C is Pathogenic according to our data. Variant chr1-160032009-G-C is described in ClinVar as Pathogenic. ClinVar VariationId is 1288.Status of the report is no_assertion_criteria_provided, 0 stars.
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIGM	NM_145167.3	c.-270C>G		upstream_gene_variant		ENST00000368090.5	NP_660150.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIGM	ENST00000368090.5	c.-270C>G		upstream_gene_variant		6	NM_145167.3	ENSP00000357069.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000248 AC: 1 AN: 403074 Hom.: 0 Cov.: 3 AF XY: 0.00 AC XY: 0 AN XY: 212516

African (AFR) AF: 0.00 AC: 0 AN: 11642

American (AMR) AF: 0.00 AC: 0 AN: 18064

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12506

East Asian (EAS) AF: 0.00 AC: 0 AN: 25908

South Asian (SAS) AF: 0.00 AC: 0 AN: 45778

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29564

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1756

European-Non Finnish (NFE) AF: 0.00000426 AC: 1 AN: 234916

Other (OTH) AF: 0.00 AC: 0 AN: 22940

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency Pathogenic:1

Apr 19, 2007

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	19
DANN	Benign	0.94
PhyloP100		3.9
PromoterAI		-0.47	Neutral

Splicing

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

Other links and lift over

dbSNP: rs587776528; hg19: chr1-160001799;