19-7163054-G-T

Position:

• chr19-7163054-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP2

The NM_000208.4(INSR):​c.2007C>A​(p.Phe669Leu) variant causes a missense 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.

• Frequency: Genomes: not found (cov: 30)
• Consequence: INSR NM_000208.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

Genes affected

INSR (HGNC:6091): (insulin receptor) This gene encodes a member of the receptor tyrosine kinase family of proteins. The encoded preproprotein is proteolytically processed to generate alpha and beta subunits that form a heterotetrameric receptor. Binding of insulin or other ligands to this receptor activates the insulin signaling pathway, which regulates glucose uptake and release, as well as the synthesis and storage of carbohydrates, lipids and protein. Mutations in this gene underlie the inherited severe insulin resistance syndromes including type A insulin resistance syndrome, Donohue syndrome and Rabson-Mendenhall syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2015]

INSR (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), INSR. . Gene score misZ 3.8314 (greater than the threshold 3.09). Trascript score misZ 5.4593 (greater than threshold 3.09). GenCC has associacion of gene with insulin-resistance syndrome type A, hyperinsulinism due to INSR deficiency, Rabson-Mendenhall syndrome, Donohue syndrome.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
INSR	NM_000208.4	c.2007C>A	p.Phe669Leu	missense_variant	9/22	ENST00000302850.10	NP_000199.2
INSR	NM_001079817.3	c.2007C>A	p.Phe669Leu	missense_variant	9/21		NP_001073285.1
INSR	XM_011527988.3	c.2007C>A	p.Phe669Leu	missense_variant	9/22		XP_011526290.2
INSR	XM_011527989.4	c.2007C>A	p.Phe669Leu	missense_variant	9/21		XP_011526291.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
INSR	ENST00000302850.10	c.2007C>A	p.Phe669Leu	missense_variant	9/22	1	NM_000208.4	ENSP00000303830.4
INSR	ENST00000341500.9	c.2007C>A	p.Phe669Leu	missense_variant	9/21	1		ENSP00000342838.4
INSR	ENST00000598216.1	n.1982C>A		non_coding_transcript_exon_variant	9/10	1
INSR	ENST00000600492.1	c.408C>A	p.Phe136Leu	missense_variant	3/4	5		ENSP00000473170.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.84
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.39
CADD	Benign	1.5
DANN	Uncertain	0.98
DEOGEN2	Uncertain	0.75	.;D;T
Eigen	Benign	-0.94
Eigen_PC	Benign	-0.97
FATHMM_MKL	Uncertain	0.85	D
LIST_S2	Uncertain	0.92	D;D;D
M_CAP	Benign	0.025	T
MetaRNN	Uncertain	0.56	D;D;D
MetaSVM	Benign	-0.93	T
MutationAssessor	Benign	1.5	L;L;.
PrimateAI	Uncertain	0.69	T
PROVEAN	Uncertain	-3.2	D;D;.
REVEL	Benign	0.16
Sift	Benign	0.11	T;T;.
Sift4G	Benign	0.31	T;T;D
Polyphen		0.0010	B;B;.
Vest4		0.26
MutPred		0.68		Loss of sheet (P = 0.0817);Loss of sheet (P = 0.0817);.;
MVP		0.72
MPC		0.89
ClinPred		0.69	D
GERP RS		-4.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.34
gMVP		0.45

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: rs2962; hg19: chr19-7163065;