rs1279159853

Variant names:

• chr19-8364506-C-A
• rs1279159853
• NM_139314.3:c.185C>A

Your query was ambiguous. Multiple possible variants found:

• chr19-8364506-C-A
• chr19-8364506-C-G
• chr19-8364506-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_139314.3(ANGPTL4):​c.185C>A​(p.Thr62Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000000708 in 1,412,096 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T62I) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.1e-7 (0 hom.)
• Consequence: ANGPTL4 NM_139314.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.02

Genes affected

ANGPTL4 (HGNC:16039): (angiopoietin like 4) This gene encodes a glycosylated, secreted protein containing a C-terminal fibrinogen domain. The encoded protein is induced by peroxisome proliferation activators and functions as a serum hormone that regulates glucose homeostasis, lipid metabolism, and insulin sensitivity. This protein can also act as an apoptosis survival factor for vascular endothelial cells and can prevent metastasis by inhibiting vascular growth and tumor cell invasion. The C-terminal domain may be proteolytically-cleaved from the full-length secreted protein. Decreased expression of this gene has been associated with type 2 diabetes. Alternative splicing results in multiple transcript variants. This gene was previously referred to as ANGPTL2 but has been renamed ANGPTL4. [provided by RefSeq, Sep 2013]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANGPTL4	NM_139314.3	c.185C>A	p.Thr62Asn	missense_variant	Exon 1 of 7	ENST00000301455.7	NP_647475.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANGPTL4	ENST00000301455.7	c.185C>A	p.Thr62Asn	missense_variant	Exon 1 of 7	1	NM_139314.3	ENSP00000301455.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.08e-7 AC: 1 AN: 1412096 Hom.: 0 Cov.: 32 AF XY: 0.00000143 AC XY: 1 AN XY: 698030

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.19e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.27
BayesDel_addAF	Benign	0.0075	T
BayesDel_noAF	Benign	-0.23
CADD	Pathogenic	27
DANN	Uncertain	0.99
DEOGEN2	Benign	0.19	.;.;T;D;.
Eigen	Uncertain	0.61
Eigen_PC	Uncertain	0.56
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Benign	0.78	T;T;T;.;T
M_CAP	Pathogenic	0.59	D
MetaRNN	Uncertain	0.65	D;D;D;D;D
MetaSVM	Benign	-0.54	T
MutationAssessor	Pathogenic	3.1	.;.;.;M;M
PrimateAI	Pathogenic	0.88	D
PROVEAN	Uncertain	-3.1	.;.;.;D;D
REVEL	Uncertain	0.30
Sift	Uncertain	0.0030	.;.;.;D;D
Sift4G	Pathogenic	0.0	D;D;D;D;D
Polyphen		0.99	.;.;.;D;.
Vest4		0.62, 0.65
MutPred		0.43		Loss of phosphorylation at T62 (P = 0.0407);Loss of phosphorylation at T62 (P = 0.0407);Loss of phosphorylation at T62 (P = 0.0407);Loss of phosphorylation at T62 (P = 0.0407);Loss of phosphorylation at T62 (P = 0.0407);
MVP		0.91
MPC		0.70
ClinPred		0.98	D
GERP RS		5.0
Varity_R		0.45
gMVP		0.89

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1279159853; hg19: chr19-8429390;