3-15455920-C-G

Variant names:

• chr3-15455920-C-G
• rs749266800
• NM_005677.4:c.1174G>C

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 3P and 1B. PM2 PP2 BP4

The NM_005677.4(COLQ):​c.1174G>C​(p.Asp392His) 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. 13/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D392N) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: COLQ NM_005677.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 0 publications found

Genes affected

COLQ (HGNC:2226): (collagen like tail subunit of asymmetric acetylcholinesterase) This gene encodes the subunit of a collagen-like molecule associated with acetylcholinesterase in skeletal muscle. Each molecule is composed of three identical subunits. Each subunit contains a proline-rich attachment domain (PRAD) that binds an acetylcholinesterase tetramer to anchor the catalytic subunit of the enzyme to the basal lamina. Mutations in this gene are associated with endplate acetylcholinesterase deficiency. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

COLQ Gene-Disease associations (from GenCC):

• congenital myasthenic syndrome 5

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, PanelApp Australia

ENSG00000293553 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 16 curated pathogenic missense variants (we use a threshold of 10). The gene has 5 curated benign missense variants. Gene score misZ: -0.21928 (below the threshold of 3.09). Trascript score misZ: -0.17745 (below the threshold of 3.09). GenCC associations: The gene is linked to congenital myasthenic syndrome 5.
• BP4: Computational evidence support a benign effect (MetaRNN=0.33409846).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLQ	NM_005677.4	c.1174G>C	p.Asp392His	missense_variant	Exon 15 of 17	ENST00000383788.10	NP_005668.2
COLQ	NM_080538.2	c.1144G>C	p.Asp382His	missense_variant	Exon 15 of 17		NP_536799.1
COLQ	NM_080539.4	c.1072G>C	p.Asp358His	missense_variant	Exon 14 of 16		NP_536800.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COLQ	ENST00000383788.10	c.1174G>C	p.Asp392His	missense_variant	Exon 15 of 17	1	NM_005677.4	ENSP00000373298.3
COLQ	ENST00000603808.5	c.1174G>C	p.Asp392His	missense_variant	Exon 15 of 17	1		ENSP00000474271.1
ENSG00000293553	ENST00000629729.3	n.21G>C		non_coding_transcript_exon_variant	Exon 1 of 6	5		ENSP00000518887.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Uncertain	0.032	T
BayesDel_noAF	Benign	-0.19
CADD	Benign	20
DANN	Benign	0.95
DEOGEN2	Benign	0.36	T;.;.;.
Eigen	Benign	-0.42
Eigen_PC	Benign	-0.60
FATHMM_MKL	Benign	0.18	N
LIST_S2	Pathogenic	0.98	D;D;D;D
M_CAP	Uncertain	0.17	D
MetaRNN	Benign	0.33	T;T;T;T
MetaSVM	Uncertain	0.023	D
MutationAssessor	Benign	1.1	L;.;.;.
PhyloP100		0.10
PrimateAI	Benign	0.33	T
PROVEAN	Benign	-1.5	N;N;.;N
REVEL	Uncertain	0.41
Sift	Uncertain	0.013	D;D;.;.
Sift4G	Uncertain	0.0070	D;D;D;D
Polyphen		0.98	D;D;.;D
Vest4		0.37
MutPred		0.43		Loss of stability (P = 0.1185);.;Loss of stability (P = 0.1185);.;
MVP		0.85
MPC		0.12
ClinPred		0.27	T
GERP RS		-1.8
Varity_R		0.091
gMVP		0.59
Mutation Taster		=92/8	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.14		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs749266800; hg19: chr3-15497427;