10-30626218-T-C

Position:

• chr10-30626218-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_183058.3(LYZL2):​c.185A>G​(p.Gln62Arg) 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. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: LYZL2 NM_183058.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.272

Genes affected

LYZL2 (HGNC:29613): (lysozyme like 2) Lysozymes (see LYZ; MIM 153450), especially C-type lysozymes, are well-recognized bacteriolytic factors widely distributed in the animal kingdom and play a mainly protective role in host defense. LYZL2 is a member of a family of lysozyme-like genes (Zhang et al., 2005 [PubMed 16014814]).[supplied by OMIM, Apr 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.16136882).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LYZL2	NM_183058.3	c.185A>G	p.Gln62Arg	missense_variant	3/5	ENST00000647634.2	NP_898881.3
LYZL2	XM_011519306.3	c.323A>G	p.Gln108Arg	missense_variant	3/4		XP_011517608.1
LYZL2	XM_011519307.3	c.323A>G	p.Gln108Arg	missense_variant	3/4		XP_011517609.1
LYZL2	XR_930469.3	n.371A>G		non_coding_transcript_exon_variant	3/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LYZL2	ENST00000647634.2	c.185A>G	p.Gln62Arg	missense_variant	3/5		NM_183058.3	ENSP00000497408	P1
LYZL2	ENST00000375318.4	c.323A>G	p.Gln108Arg	missense_variant	3/5	1		ENSP00000364467

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jan 30, 2024

The c.323A>G (p.Q108R) alteration is located in exon 3 (coding exon 3) of the LYZL2 gene. This alteration results from a A to G substitution at nucleotide position 323, causing the glutamine (Q) at amino acid position 108 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.087
BayesDel_addAF	Benign	-0.089	T
BayesDel_noAF	Benign	-0.37
CADD	Benign	4.1
DANN	Benign	0.90
DEOGEN2	Benign	0.014	T;.
Eigen	Benign	-0.74
Eigen_PC	Benign	-0.82
FATHMM_MKL	Benign	0.020	N
LIST_S2	Benign	0.26	T;T
M_CAP	Benign	0.0077	T
MetaRNN	Benign	0.16	T;T
MetaSVM	Benign	-0.92	T
MutationAssessor	Benign	1.3	L;.
MutationTaster	Benign	1.0	N
PrimateAI	Benign	0.42	T
PROVEAN	Benign	-0.78	.;N
REVEL	Benign	0.16
Sift	Benign	0.079	.;T
Sift4G	Benign	0.29	.;T
Polyphen		0.57	.;P
Vest4		0.24
MutPred		0.54		.;Gain of sheet (P = 0.1208);
MVP		0.21
MPC		0.16
ClinPred		0.13	T
GERP RS		2.3
Varity_R		0.040
gMVP		0.45

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-30915147;