rs121908261

Variant names:

• chr11-2160809-G-A
• rs121908261
• NM_000207.3:c.163C>T

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM1 PM2 PP3_Moderate PP5_Very_Strong

The NM_000207.3(INS):​c.163C>T​(p.Arg55Cys) 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 pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely risk allele (★★).

• Frequency: Genomes: not found (cov: 35)
• Consequence: INS NM_000207.3 missense
• Clinical Significance: Pathogenic/Likely pathogenic/Likely risk allele criteria provided, multiple submitters, no conflicts P:7 O:1
• Conservation: PhyloP100: 3.08

Genes affected

INS (HGNC:6081): (insulin) This gene encodes insulin, a peptide hormone that plays a vital role in the regulation of carbohydrate and lipid metabolism. After removal of the precursor signal peptide, proinsulin is post-translationally cleaved into three peptides: the B chain and A chain peptides, which are covalently linked via two disulfide bonds to form insulin, and C-peptide. Binding of insulin to the insulin receptor (INSR) stimulates glucose uptake. A multitude of mutant alleles with phenotypic effects have been identified, including insulin-dependent diabetes mellitus, permanent neonatal diabetes diabetes mellitus, maturity-onset diabetes of the young type 10 and hyperproinsulinemia. There is a read-through gene, INS-IGF2, which overlaps with this gene at the 5' region and with the IGF2 gene at the 3' region. [provided by RefSeq, May 2020]

INS-IGF2 (HGNC:33527): (INS-IGF2 readthrough) This locus includes two alternatively spliced read-through transcript variants which align to the INS gene in the 5' region and to the IGF2 gene in the 3' region. One transcript is predicted to encode a protein which shares the N-terminus with the INS protein but has a distinct and longer C-terminus, whereas the other transcript is a candidate for nonsense-mediated decay (NMD). The transcripts are imprinted and are paternally expressed in the limb and eye. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 14 ACMG points.

• PM1: In a disulfide_bond Interchain (between B and A chains) (size 65) in uniprot entity INS_HUMAN there are 10 pathogenic changes around while only 1 benign (91%) in NM_000207.3
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.926
• PP5: Variant 11-2160809-G-A is Pathogenic according to our data. Variant chr11-2160809-G-A is described in ClinVar as [Likely_risk_allele]. Clinvar id is 13392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=2, Likely_risk_allele=1, Pathogenic=2, not_provided=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
INS	NM_000207.3	c.163C>T	p.Arg55Cys	missense_variant	Exon 2 of 3	ENST00000381330.5	NP_000198.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
INS	ENST00000381330.5	c.163C>T	p.Arg55Cys	missense_variant	Exon 2 of 3	1	NM_000207.3	ENSP00000370731.5
INS-IGF2	ENST00000397270.1	c.163C>T	p.Arg55Cys	missense_variant	Exon 2 of 5	1		ENSP00000380440.1

Frequencies

GnomAD3 genomes Cov.: 35

GnomAD4 exome Cov.: 88

GnomAD4 genome Cov.: 35

ClinVar

Significance: Pathogenic/Likely pathogenic/Likely risk allele

Submissions summary: Pathogenic:7 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:3

Nov 05, 2021

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Published functional studies demonstrate that R55C leads to the reduction of proinsulin secretion from the ER and potential activation of the ER stress response (Meur et al., 2010; Liu et al., 2010); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at a significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 23624530, 20938745, 20007936, 20948967, 27913849, 25721872, 20226046, 18192540) -

Apr 30, 2019

Genetic Services Laboratory, University of Chicago

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

DNA sequence analysis of the INS gene demonstrated a sequence change, c.163C>T, in exon 2 that results in an amino acid change, p.Arg55Cys. The p.Arg55Cys change affects a moderately conserved amino acid residue located in a domain of the INS protein that is known to be functional. The p.Arg55Cys substitution appears to be deleterious using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL). The p.Arg55Cys change has been reported in a mother and daughter with type 1 diabetes with onset at 13 and 10 years of age; the p.Arg55Cys change was found to be a de novo change in the mother (PMID: 18192540). This sequence change has been described in the gnomAD database with a very low population frequency of 0.0004% (dbSNP rs121908261). -

Mar 10, 2022

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Experimental studies have shown that this missense change affects INS function (PMID: 20007936, 20948967). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 13392). This missense change has been observed in individual(s) with autosomal dominant INS-related conditions (PMID: 18192540, 20007936; Invitae). It has also been observed to segregate with disease in related individuals. This variant is present in population databases (rs121908261, gnomAD 0.0009%). This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 55 of the INS protein (p.Arg55Cys). -

Type 1 diabetes mellitus 2 Pathogenic:1 Other:1

-

UniProtKB/Swiss-Prot

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

Apr 01, 2008

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Monogenic diabetes Pathogenic:1

Jan 19, 2024

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: INS c.163C>T (p.Arg55Cys) results in a non-conservative amino acid change located in the Insulin-like domain (IPR016179) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The frequency data for this variant in gnomAD is considered unreliable, as metrics indicate poor data quality at this position. c.163C>T has been reported in the literature in multiple individuals affected with Monogenic Diabetes (example: Molven_2008, Meur_2010, Petruzelkova_2016, Colclough_2022). The variant segregated with the disease in two independent families (Molven_2008, and Meur_2010) and at-least one case is reported as a de novo occurrence (Molven_2008). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence that R55C leads to the reduction of proinsulin secretion from the ER (Meur_2010). The following publications have been ascertained in the context of this evaluation (PMID: 26641800, 34789499, 20007936, 18192540). ClinVar contains an entry for this variant (Variation ID: 13392). Based on the evidence outlined above, the variant was classified as pathogenic. -

INS-related disorder Pathogenic:1

Jul 19, 2024

PreventionGenetics, part of Exact Sciences

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The INS c.163C>T variant is predicted to result in the amino acid substitution p.Arg55Cys. This variant has been reported in an individual with autoantibody-negative type 1 diabetes (Molven et al. 2008. PubMed ID: 18192540) and in several individuals with clinical features consistent with mature onset diabetes of the young (MODY) (Meur et al. 2009. PubMed ID: 20007936; Colclough et al. 2022. PubMed ID: 34789499; Yorifuji et al. 2022. PubMed ID: 36504295). In two families, there was evidence of segregation with diabetes (Molven et al. 2008. PubMed ID: 18192540; Meur et al. 2009. PubMed ID: 20007936). In one of the aforementioned families, the proband's mother had diabetes and was found to be de novo, yet the maternal grandfather had diabetes of unknown etiology (Molven et al. 2008. PubMed ID: 18192540). In vitro functional studies demonstrate reduced proinsulin secretion, ER retention, and ER stress (Meur et al. 2009. PubMed ID: 20007936). This variant is reported in 0.00091% of alleles in individuals of European (non-Finnish) descent in gnomAD; however, the quality of this data is questionable and should be treated with caution. This variant is interpreted as pathogenic. -

Diabetes mellitus type 1 Pathogenic:1

-

Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic

Significance: Likely risk allele

Review Status: criteria provided, single submitter

Collection Method: research

Potent mutations in the INS gene can cause early onset diabetes mellitus which is insulin dependent. May have poor response to sulfonylureas, mutations in this gene can cause beta cell destruction. Sufficient evidence is found to confer the association of this particular variant rs121908261 with type1B Diabetes mellitus. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.83
BayesDel_addAF	Pathogenic	0.42	D
BayesDel_noAF	Pathogenic	0.37
CADD	Pathogenic	32
DANN	Pathogenic	1.0
DEOGEN2	Uncertain	0.73	D;D;D;D;.;.
Eigen	Uncertain	0.47
Eigen_PC	Uncertain	0.31
FATHMM_MKL	Uncertain	0.78	D
LIST_S2	Uncertain	0.92	D;.;.;D;D;D
M_CAP	Pathogenic	0.82	D
MetaRNN	Pathogenic	0.93	D;D;D;D;D;D
MetaSVM	Pathogenic	0.90	D
MutationAssessor	Benign	0.69	N;.;.;.;.;.
PROVEAN	Uncertain	-4.0	D;D;D;D;D;D
REVEL	Pathogenic	0.82
Sift	Pathogenic	0.0	D;D;D;D;D;D
Sift4G	Pathogenic	0.0	D;D;D;D;.;D
Polyphen		1.0	D;D;D;D;.;D
Vest4		0.47
MutPred		0.71		Loss of disorder (P = 0.0143);Loss of disorder (P = 0.0143);Loss of disorder (P = 0.0143);Loss of disorder (P = 0.0143);Loss of disorder (P = 0.0143);Loss of disorder (P = 0.0143);
MVP		0.91
MPC		1.0
ClinPred		0.98	D
GERP RS		3.1
Varity_R		0.97
gMVP		0.88

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: rs121908261; hg19: chr11-2182039;