3-9944066-CAG-GAA

Variant names:

• chr3-9944066-CAG-GAA
• ENST00000326434.9:c.1213_1215delCAGinsGAA
• CRELD1 p.Gln405Glu

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001374317.1(CRELD1):​c.1225_1227delCAGinsGAA​(p.Gln409Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CRELD1 NM_001374317.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554
• Publications: 0 publications found

Genes affected

CRELD1 (HGNC:14630): (cysteine rich with EGF like domains 1) This gene encodes a member of a subfamily of epidermal growth factor-related proteins. The encoded protein is characterized by a cysteine-rich with epidermal growth factor-like domain. This protein may function as a cell adhesion molecule. Mutations in this gene are the cause of atrioventricular septal defect. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Apr 2010]

ENSG00000288550 (HGNC:):

PRRT3 (HGNC:26591): (proline rich transmembrane protein 3) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001374317.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRELD1	NM_001077415.3	MANE Select	c.1049-299_1049-297delCAGinsGAA		intron	N/A	NP_001070883.2	Q96HD1-1
	CRELD1	NM_001374317.1		c.1225_1227delCAGinsGAA	p.Gln409Glu	missense	N/A	NP_001361246.1	A0A804HJJ0
	CRELD1	NM_001374318.1		c.1225_1227delCAGinsGAA	p.Gln409Glu	missense	N/A	NP_001361247.1	A0A804HJJ0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRELD1	ENST00000326434.9	TSL:1	c.1213_1215delCAGinsGAA	p.Gln405Glu	missense	N/A	ENSP00000321856.5	Q96HD1-2
	CRELD1	ENST00000452070.6	TSL:2 MANE Select	c.1049-299_1049-297delCAGinsGAA		intron	N/A	ENSP00000393643.2	Q96HD1-1
	CRELD1	ENST00000383811.8	TSL:1	c.1049-299_1049-297delCAGinsGAA		intron	N/A	ENSP00000373322.3	Q96HD1-1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.55

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr3-9985750;

Mutation Effect Viewer