1-113980534-G-C

Variant names:

• chr1-113980534-G-C
• NM_020190.5:c.317G>C

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP3_Moderate

The NM_020190.5(OLFML3):​c.317G>C​(p.Cys106Ser) variant causes a missense 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 Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: OLFML3 NM_020190.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 9.52

Genes affected

OLFML3 (HGNC:24956): (olfactomedin like 3) This gene encodes a member of the olfactomedin-like gene family which also includes genes encoding noelin, tiarin, myocilin, amassin, optimedin, photomedin, and latrophilin. The encoded protein is a secreted extracellular matrix glycoprotein with a C-terminal olfactomedin domain that facilitates protein-protein interactions, cell adhesion, and intercellular interactions. It serves as both a scaffold protein that recruits bone morphogenetic protein 1 to its substrate chordin, and as a vascular tissue remodeler with pro-angiogenic properties. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.874

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OLFML3	NM_020190.5	c.317G>C	p.Cys106Ser	missense_variant	Exon 2 of 3	ENST00000320334.5	NP_064575.1
OLFML3	NM_001286352.3	c.257G>C	p.Cys86Ser	missense_variant	Exon 3 of 4		NP_001273281.1
OLFML3	NM_001286353.3	c.134G>C	p.Cys45Ser	missense_variant	Exon 2 of 3		NP_001273282.1
OLFML3	XM_017001848.3	c.257G>C	p.Cys86Ser	missense_variant	Exon 2 of 3		XP_016857337.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OLFML3	ENST00000320334.5	c.317G>C	p.Cys106Ser	missense_variant	Exon 2 of 3	1	NM_020190.5	ENSP00000322273.4

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

Sep 03, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.317G>C (p.C106S) alteration is located in exon 2 (coding exon 2) of the OLFML3 gene. This alteration results from a G to C substitution at nucleotide position 317, causing the cysteine (C) at amino acid position 106 to be replaced by a serine (S). 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	Pathogenic	0.93
BayesDel_addAF	Pathogenic	0.49	D
BayesDel_noAF	Pathogenic	0.47
CADD	Pathogenic	27
DANN	Uncertain	0.99
DEOGEN2	Benign	0.13	T;.;T
Eigen	Pathogenic	0.76
Eigen_PC	Pathogenic	0.79
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Benign	0.80	T;T;T
M_CAP	Uncertain	0.15	D
MetaRNN	Pathogenic	0.87	D;D;D
MetaSVM	Pathogenic	0.85	D
MutationAssessor	Benign	1.8	.;.;L
PrimateAI	Uncertain	0.75	T
PROVEAN	Pathogenic	-5.3	.;D;D
REVEL	Pathogenic	0.92
Sift	Uncertain	0.010	.;D;D
Sift4G	Uncertain	0.055	T;T;T
Polyphen		1.0, 1.0	.;D;D
Vest4		0.89
MutPred		0.64		.;.;Loss of catalytic residue at P105 (P = 0.0068);
MVP		0.90
MPC		0.77
ClinPred		0.99	D
GERP RS		5.6
Varity_R		0.73
gMVP		0.60

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: chr1-114523156;