16-71947511-CTTTG-CTTTGTTTG

Variant names:

• chr16-71947511-C-CTTTG
• rs149635567
• NM_181536.2:c.3695_3698dupCAAA

Variant summary

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

The NM_181536.2(PKD1L3):​c.3695_3698dupCAAA​(p.Lys1233AsnfsTer21) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 19)
• Consequence: PKD1L3 NM_181536.2 frameshift
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488

Genes affected

PKD1L3 (HGNC:21716): (polycystin 1 like 3, transient receptor potential channel interacting) This gene encodes a member of the polycystin protein family. The encoded protein contains 11 transmembrane domains, a latrophilin/CL-1-like GPCR proteolytic site (GPS) domain, and a polycystin-1, lipoxygenase, alpha-toxin (PLAT) domain. This protein may function as a component of cation channel pores.[provided by RefSeq, Apr 2009]

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
PKD1L3	NM_181536.2	c.3695_3698dupCAAA	p.Lys1233AsnfsTer21	frameshift_variant	Exon 22 of 30	ENST00000620267.2	NP_853514.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PKD1L3	ENST00000620267.2	c.3695_3698dupCAAA	p.Lys1233AsnfsTer21	frameshift_variant	Exon 22 of 30	1	NM_181536.2	ENSP00000480090.1

Frequencies

GnomAD3 genomes Cov.: 19

GnomAD3 exomes AF: 0.792 AC: 124156 AN: 156688 Hom.: 49879 AF XY: 0.796 AC XY: 66019 AN XY: 82920

Gnomad AFR exome AF: 0.596

Gnomad AMR exome AF: 0.847

Gnomad ASJ exome AF: 0.822

Gnomad EAS exome AF: 0.972

Gnomad SAS exome AF: 0.849

Gnomad FIN exome AF: 0.796

Gnomad NFE exome AF: 0.738

Gnomad OTH exome AF: 0.779

GnomAD4 exome Cov.: 22

GnomAD4 genome Cov.: 19

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs149635567; hg19: chr16-71981414;