1-201316631-G-C

Variant names:

• chr1-201316631-G-C
• rs1779297
• NM_001005337.3:c.780G>C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001005337.3(PKP1):​c.780G>C​(p.Lys260Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 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. K260M) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: PKP1 NM_001005337.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38

Genes affected

PKP1 (HGNC:9023): (plakophilin 1) This gene encodes a member of the arm-repeat (armadillo) and plakophilin gene families. Plakophilin proteins contain numerous armadillo repeats, localize to cell desmosomes and nuclei, and participate in linking cadherins to intermediate filaments in the cytoskeleton. This protein may be involved in molecular recruitment and stabilization during desmosome formation. Mutations in this gene have been associated with the ectodermal dysplasia/skin fragility syndrome. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.12784159).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PKP1	NM_001005337.3	c.780G>C	p.Lys260Asn	missense_variant	Exon 4 of 14	ENST00000367324.8	NP_001005337.1
PKP1	NM_000299.4	c.780G>C	p.Lys260Asn	missense_variant	Exon 4 of 15		NP_000290.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PKP1	ENST00000367324.8	c.780G>C	p.Lys260Asn	missense_variant	Exon 4 of 14	1	NM_001005337.3	ENSP00000356293.4
PKP1	ENST00000263946.7	c.780G>C	p.Lys260Asn	missense_variant	Exon 4 of 15	5		ENSP00000263946.3
PKP1	ENST00000352845.3	c.780G>C	p.Lys260Asn	missense_variant	Exon 4 of 14	5		ENSP00000295597.3
PKP1	ENST00000475988.1	n.122G>C		non_coding_transcript_exon_variant	Exon 2 of 5	3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.56
BayesDel_noAF	Benign	-0.65
CADD	Benign	20
DEOGEN2	Benign	0.017	.;T;T
LIST_S2	Benign	0.82	T;T;.
MetaRNN	Benign	0.13	T;T;T
PROVEAN	Benign	-0.68	N;N;N
Sift	Benign	0.30	T;T;T
Sift4G	Benign	0.47	T;T;T
Vest4		0.18
gMVP		0.26

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: rs1779297; hg19: chr1-201285759;