chr19-1223069-G-C

Variant names:

• chr19-1223069-G-C
• rs1555739243
• NM_000455.5:c.1005G>C

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_000455.5(STK11):​c.1005G>C​(p.Met335Ile) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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 Uncertain significance in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M335V) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: STK11 NM_000455.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.58

Genes affected

STK11 (HGNC:11389): (serine/threonine kinase 11) The protein encoded by this gene is a serine/threonine kinase that regulates cell polarity and energy metabolism and functions as a tumor suppressor. Mutations in this gene have been associated with the autosomal dominant Peutz-Jeghers syndrome, as well as with skin, pancreatic, and testicular cancers. [provided by RefSeq, May 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 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
STK11	NM_000455.5	c.1005G>C	p.Met335Ile	missense_variant	Exon 8 of 10	ENST00000326873.12	NP_000446.1
STK11	NM_001407255.1	c.1005G>C	p.Met335Ile	missense_variant	Exon 8 of 9		NP_001394184.1
STK11	NR_176325.1	n.2272G>C		non_coding_transcript_exon_variant	Exon 9 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK11	ENST00000326873.12	c.1005G>C	p.Met335Ile	missense_variant	Exon 8 of 10	1	NM_000455.5	ENSP00000324856.6
STK11	ENST00000652231.1	c.1005G>C	p.Met335Ile	missense_variant	Exon 8 of 9			ENSP00000498804.1
STK11	ENST00000585748.3	c.633G>C	p.Met211Ile	missense_variant	Exon 10 of 12	3		ENSP00000477641.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.98
BayesDel_addAF	Uncertain	0.079	D
BayesDel_noAF	Benign	-0.12
CADD	Uncertain	25
DANN	Uncertain	0.98
DEOGEN2	Benign	0.35	T;D
Eigen	Benign	0.024
Eigen_PC	Benign	0.071
FATHMM_MKL	Benign	0.66	D
LIST_S2	Uncertain	0.96	D;D
M_CAP	Uncertain	0.16	D
MetaRNN	Uncertain	0.49	T;T
MetaSVM	Benign	-0.41	T
MutationAssessor	Benign	2.0	.;M
PrimateAI	Uncertain	0.65	T
PROVEAN	Uncertain	-2.6	.;D
REVEL	Uncertain	0.46
Sift	Benign	0.20	.;T
Sift4G	Benign	0.30	T;T
Polyphen		0.30	.;B
Vest4		0.65
MutPred		0.41		Loss of disorder (P = 0.0963);Loss of disorder (P = 0.0963);
MVP		0.62
MPC		0.072
ClinPred		0.85	D
GERP RS		3.8
PromoterAI		-0.087
Varity_R		0.62
gMVP		0.56
Mutation Taster		=63/37	polymorphism

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: rs1555739243; hg19: chr19-1223068;