chr3-9917383-G-C

Position:

• chr3-9917383-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_153460.4(IL17RC):​c.68G>C​(p.Arg23Thr) 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. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R23S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: IL17RC NM_153460.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.732

Genes affected

IL17RC (HGNC:18358): (interleukin 17 receptor C) This gene encodes a single-pass type I membrane protein that shares similarity with the interleukin-17 receptor (IL-17RA). Unlike IL-17RA, which is predominantly expressed in hemopoietic cells, and binds with high affinity to only IL-17A, this protein is expressed in nonhemopoietic tissues, and binds both IL-17A and IL-17F with similar affinities. The proinflammatory cytokines, IL-17A and IL-17F, have been implicated in the progression of inflammatory and autoimmune diseases. Multiple alternatively spliced transcript variants encoding different isoforms have been detected for this gene, and it has been proposed that soluble, secreted proteins lacking transmembrane and intracellular domains may function as extracellular antagonists to cytokine signaling. [provided by RefSeq, Feb 2011]

(HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2744767).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL17RC	NM_153460.4	c.68G>C	p.Arg23Thr	missense_variant	1/19	ENST00000403601.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL17RC	ENST00000403601.8	c.68G>C	p.Arg23Thr	missense_variant	1/19	1	NM_153460.4	P4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Candidiasis, familial, 9 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jul 05, 2022

ClinVar contains an entry for this variant (Variation ID: 1488363). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with IL17RC-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with threonine, which is neutral and polar, at codon 23 of the IL17RC protein (p.Arg23Thr). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Benign	0.000095	T
BayesDel_noAF	Benign	-0.24
CADD	Benign	21
DANN	Benign	0.94
DEOGEN2	Benign	0.11	.;.;.;T;.;.;.;.;.
Eigen	Benign	-0.054
Eigen_PC	Benign	-0.032
FATHMM_MKL	Benign	0.36	N
LIST_S2	Uncertain	0.92	D;.;D;D;D;D;D;D;D
M_CAP	Benign	0.065	D
MetaRNN	Benign	0.27	T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.92	T
MutationAssessor	Uncertain	2.0	M;M;.;M;M;.;M;M;M
MutationTaster	Benign	1.0	D;N;N;N;N;N
PrimateAI	Benign	0.40	T
PROVEAN	Uncertain	-2.8	.;D;D;N;.;D;D;D;D
REVEL	Benign	0.18
Sift	Uncertain	0.0030	.;D;D;D;.;D;D;D;D
Sift4G	Uncertain	0.0050	D;D;D;D;.;D;D;D;D
Polyphen		0.59, 0.91, 0.79	.;P;.;P;P;.;P;.;.
Vest4		0.46
MutPred		0.58		Gain of glycosylation at S20 (P = 0.0545);Gain of glycosylation at S20 (P = 0.0545);Gain of glycosylation at S20 (P = 0.0545);Gain of glycosylation at S20 (P = 0.0545);Gain of glycosylation at S20 (P = 0.0545);Gain of glycosylation at S20 (P = 0.0545);Gain of glycosylation at S20 (P = 0.0545);Gain of glycosylation at S20 (P = 0.0545);Gain of glycosylation at S20 (P = 0.0545);
MVP		0.27
MPC		0.48
ClinPred		0.80	D
GERP RS		3.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Varity_R		0.45
gMVP		0.32

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: chr3-9959067;