rs398122987

Variant names:

• chr1-62597996-CAACT-C
• rs398122987
• NM_014495.4:c.439_442delAACT

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_014495.4(ANGPTL3):​c.439_442delAACT​(p.Asn147fs) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000198 in 1,567,704 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: 𝑓 0.000092 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00021 (1 hom.)
• Consequence: ANGPTL3 NM_014495.4 frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: 7.61

Genes affected

ANGPTL3 (HGNC:491): (angiopoietin like 3) This gene encodes a member of a family of secreted proteins that function in angiogenesis. The encoded protein, which is expressed predominantly in the liver, is further processed into an N-terminal coiled-coil domain-containing chain and a C-terminal fibrinogen chain. The N-terminal chain is important for lipid metabolism, while the C-terminal chain may be involved in angiogenesis. Mutations in this gene cause familial hypobetalipoproteinemia type 2. [provided by RefSeq, Aug 2015]

DOCK7 (HGNC:19190): (dedicator of cytokinesis 7) The protein encoded by this gene is a guanine nucleotide exchange factor (GEF) that plays a role in axon formation and neuronal polarization. The encoded protein displays GEF activity toward RAC1 and RAC3 Rho small GTPases but not toward CDC42. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 1-62597996-CAACT-C is Pathogenic according to our data. Variant chr1-62597996-CAACT-C is described in ClinVar as [Pathogenic]. Clinvar id is 91865.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-62597996-CAACT-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANGPTL3	NM_014495.4	c.439_442delAACT	p.Asn147fs	frameshift_variant	Exon 1 of 7	ENST00000371129.4	NP_055310.1
DOCK7	NM_001367561.1	c.1683-11376_1683-11373delAGTT		intron_variant	Intron 14 of 49	ENST00000635253.2	NP_001354490.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANGPTL3	ENST00000371129.4	c.439_442delAACT	p.Asn147fs	frameshift_variant	Exon 1 of 7	1	NM_014495.4	ENSP00000360170.3
DOCK7	ENST00000635253.2	c.1683-11376_1683-11373delAGTT		intron_variant	Intron 14 of 49	5	NM_001367561.1	ENSP00000489124.1

Frequencies

GnomAD3 genomes AF: 0.0000921 AC: 14 AN: 152000 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000483

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000132

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.000172 AC: 36 AN: 208860 Hom.: 0 AF XY: 0.000192 AC XY: 22 AN XY: 114468

Gnomad AFR exome AF: 0.0000684

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000635

Gnomad SAS exome AF: 0.000385

Gnomad FIN exome AF: 0.000101

Gnomad NFE exome AF: 0.000217

Gnomad OTH exome AF: 0.000208

GnomAD4 exome AF: 0.000209 AC: 296 AN: 1415586 Hom.: 1 AF XY: 0.000219 AC XY: 154 AN XY: 703506

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000330

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000204

Gnomad4 SAS exome AF: 0.000299

Gnomad4 FIN exome AF: 0.0000577

Gnomad4 NFE exome AF: 0.000219

Gnomad4 OTH exome AF: 0.000206

GnomAD4 genome AF: 0.0000920 AC: 14 AN: 152118 Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6 AN XY: 74362

Gnomad4 AFR AF: 0.0000481

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000132

Gnomad4 OTH AF: 0.000473

Alfa AF: 0.000131 Hom.: 0

Bravo AF: 0.0000907

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Pathogenic:1

Nov 09, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Asn147*) in the ANGPTL3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ANGPTL3 are known to be pathogenic (PMID: 22247256, 24058201). This variant is present in population databases (rs749131121, gnomAD 0.04%). This premature translational stop signal has been observed in individual(s) with dyslipidemia (PMID: 22247256, 36325899). ClinVar contains an entry for this variant (Variation ID: 91865). For these reasons, this variant has been classified as Pathogenic. -

Familial hypobetalipoproteinemia 2 Pathogenic:1

Mar 01, 2012

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs398122987; hg19: chr1-63063667;