rs1555497604

Variant names:

• chr16-23452993-A-G
• rs1555497604
• NM_153603.4:c.2T>C

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PVS1_Supporting PM2 PP5_Moderate

The NM_153603.4(COG7):​c.2T>C​(p.Met1?) variant causes a start lost change involving the alteration of a 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 pathogenic (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: COG7 NM_153603.4 start_lost
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 8.26

Genes affected

COG7 (HGNC:18622): (component of oligomeric golgi complex 7) The protein encoded by this gene resides in the golgi, and constitutes one of the 8 subunits of the conserved oligomeric Golgi (COG) complex, which is required for normal golgi morphology and localization. Mutations in this gene are associated with the congenital disorder of glycosylation type IIe.[provided by RefSeq, May 2010]

ENSG00000260136 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 5 ACMG points.

• PVS1: Start lost variant, no pathogenic variants between lost start and next in-frame start position. Next in-frame start position is after 42 codons. Genomic position: 23452871. Lost 0.054 part of the original CDS.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 16-23452993-A-G is Pathogenic according to our data. Variant chr16-23452993-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 548709.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COG7	NM_153603.4	c.2T>C	p.Met1?	start_lost	Exon 1 of 17	ENST00000307149.10	NP_705831.1
LOC124903667	XR_007065030.1	n.251A>G		non_coding_transcript_exon_variant	Exon 1 of 2
COG7	XM_017023870.2	c.-277T>C		upstream_gene_variant			XP_016879359.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COG7	ENST00000307149.10	c.2T>C	p.Met1?	start_lost	Exon 1 of 17	1	NM_153603.4	ENSP00000305442.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

COG7 congenital disorder of glycosylation Pathogenic:1

Jun 29, 2018

Medical Genetics Lab, Policlinico S. Orsola.Malpighi

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Null variant (start codon) affecting gene COG7, which is a known mechanism of disease (gene COG7 is autosomal recessive). Allele not found in Broad gnomAD exomes despite good coverage=63 (greater than 20). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.25
CADD	Uncertain	26
DANN	Uncertain	0.99
DEOGEN2	Benign	0.19	T
Eigen	Uncertain	0.57
Eigen_PC	Uncertain	0.53
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Uncertain	0.90	D
M_CAP	Pathogenic	0.45	D
MetaRNN	Pathogenic	0.96	D
MetaSVM	Benign	-0.31	T
PROVEAN	Uncertain	-3.9	D
REVEL	Pathogenic	0.74
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Polyphen		1.0	D
Vest4		0.95
MutPred		0.77		Loss of stability (P = 0.0013);
MVP		0.66
ClinPred		1.0	D
GERP RS		4.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.93
gMVP		0.68

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: rs1555497604; hg19: chr16-23464314; COSMIC: COSV100207325; COSMIC: COSV100207325;