rs1057519578

Positions:

• chr12-7086404-C-G
• chr12-7086404-C-T

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1 PM2 PP5_Moderate

The NM_001733.7(C1R):​c.1092G>C​(p.Trp364Cys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: C1R NM_001733.7 missense
• Clinical Significance: Pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: 6.05

Genes affected

C1R (HGNC:1246): (complement C1r) This gene encodes a member of the peptidase S1 protein family. The encoded protein is a proteolytic subunit in the complement system C1 complex. The complement system acts as a mediator in the innate immune response by ultimately triggering phagocytosis, inflammation, and rupturing the bacterial cell wall. Mutations in this gene are associated with Ehlers-Danlos Syndrome. [provided by RefSeq, Dec 2018]

ACMG classification

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

• PM1: In a disulfide_bond (size 33) in uniprot entity C1R_HUMAN there are 6 pathogenic changes around while only 0 benign (100%) in NM_001733.7
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 12-7086404-C-G is Pathogenic according to our data. Variant chr12-7086404-C-G is described in ClinVar as [Pathogenic]. Clinvar id is 375579.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C1R	NM_001733.7	c.1092G>C	p.Trp364Cys	missense_variant	8/11	ENST00000647956.2	NP_001724.4
C1R	NM_001354346.2	c.1134G>C	p.Trp378Cys	missense_variant	8/11		NP_001341275.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C1R	ENST00000647956.2	c.1092G>C	p.Trp364Cys	missense_variant	8/11		NM_001733.7	ENSP00000497341	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, single submitter

Submissions by phenotype

Ehlers-Danlos syndrome, periodontal type 2 Pathogenic:1

Likely pathogenic, no assertion criteria provided

research

University of Washington Center for Mendelian Genomics, University of Washington

Oct 13, 2016

- -

Ehlers-Danlos syndrome, periodontal type 1 Pathogenic:1

Pathogenic, criteria provided, single submitter

research

Institute of Human Genetics, Medical University Innsbruck

Aug 23, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
CADD	Pathogenic	32
DEOGEN2	Benign	0.068	.;.;T;T;.
LIST_S2	Uncertain	0.95	D;.;D;D;D
MetaRNN	Uncertain	0.74	D;D;D;D;D
Sift4G	Uncertain	0.0040	.;.;D;.;.
Vest4		0.78, 0.79, 0.71
gMVP		0.82

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1057519578; hg19: -;