NM_203487.3:c.2866G>T

Variant names:

• chr13-67225575-C-A
• NM_203487.3:c.2866G>T

Variant summary

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

The NM_203487.3(PCDH9):​c.2866G>T​(p.Val956Phe) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,892 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: PCDH9 NM_203487.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.83

Genes affected

PCDH9 (HGNC:8661): (protocadherin 9) This gene encodes a member of the protocadherin family, and cadherin superfamily, of transmembrane proteins containing cadherin domains. These proteins mediate cell adhesion in neural tissues in the presence of calcium. The encoded protein may be involved in signaling at neuronal synaptic junctions. Sharing a characteristic with other protocadherin genes, this gene has a notably large exon that encodes multiple cadherin domains and a transmembrane region. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Nov 2012]

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
PCDH9	NM_203487.3	c.2866G>T	p.Val956Phe	missense_variant	Exon 2 of 5	ENST00000377865.7	NP_982354.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCDH9	ENST00000377865.7	c.2866G>T	p.Val956Phe	missense_variant	Exon 2 of 5	1	NM_203487.3	ENSP00000367096.2
PCDH9	ENST00000544246.5	c.2866G>T	p.Val956Phe	missense_variant	Exon 2 of 4	1		ENSP00000442186.2
PCDH9	ENST00000456367.5	c.2866G>T	p.Val956Phe	missense_variant	Exon 2 of 5	1		ENSP00000401699.2
PCDH9	ENST00000377861.4	c.2866G>T	p.Val956Phe	missense_variant	Exon 2 of 2	1		ENSP00000367092.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461892 Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1 AN XY: 727248

Gnomad4 AFR exome AF: 0.0000299

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: 0.00

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	0.19
BayesDel_addAF	Uncertain	0.032	T
BayesDel_noAF	Benign	-0.19
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.023	T;.;T;T
Eigen	Pathogenic	0.72
Eigen_PC	Pathogenic	0.72
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.95	D;D;D;D
M_CAP	Benign	0.0093	T
MetaRNN	Uncertain	0.48	T;T;T;T
MetaSVM	Benign	-0.90	T
MutationAssessor	Benign	2.0	M;M;.;.
PrimateAI	Uncertain	0.76	T
PROVEAN	Benign	-1.2	N;N;N;N
REVEL	Benign	0.18
Sift	Uncertain	0.017	D;D;D;D
Sift4G	Uncertain	0.018	D;D;D;D
Polyphen		1.0	D;D;D;D
Vest4		0.61
MutPred		0.42		Gain of catalytic residue at K959 (P = 0.004);Gain of catalytic residue at K959 (P = 0.004);Gain of catalytic residue at K959 (P = 0.004);Gain of catalytic residue at K959 (P = 0.004);
MVP		0.14
MPC		1.1
ClinPred		0.95	D
GERP RS		4.7
Varity_R		0.30
gMVP		0.50

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr13-67799707; COSMIC: COSV60568439;