NM_002958.4:c.907A>G

Variant names:

• chr3-134191957-T-C
• NM_002958.4:c.907A>G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_002958.4(RYK):​c.907A>G​(p.Ile303Val) 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 benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: RYK NM_002958.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.62

Genes affected

RYK (HGNC:10481): (receptor like tyrosine kinase) The protein encoded by this gene is an atypical member of the family of growth factor receptor protein tyrosine kinases, differing from other members at a number of conserved residues in the activation and nucleotide binding domains. This gene product belongs to a subfamily whose members do not appear to be regulated by phosphorylation in the activation segment. It has been suggested that mediation of biological activity by recruitment of a signaling-competent auxiliary protein may occur through an as yet uncharacterized mechanism. The encoded protein has a leucine-rich extracellular domain with a WIF-type Wnt binding region, a single transmembrane domain, and an intracellular tyrosine kinase domain. This protein is involved in stimulating Wnt signaling pathways such as the regulation of axon pathfinding. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Feb 2012]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2709186).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RYK	NM_002958.4	c.907A>G	p.Ile303Val	missense_variant	Exon 8 of 15	ENST00000623711.4	NP_002949.2
RYK	NM_001005861.3	c.916A>G	p.Ile306Val	missense_variant	Exon 8 of 15		NP_001005861.1
RYK	XR_007095716.1	n.1121A>G		non_coding_transcript_exon_variant	Exon 8 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RYK	ENST00000623711.4	c.907A>G	p.Ile303Val	missense_variant	Exon 8 of 15	1	NM_002958.4	ENSP00000485095.1
RYK	ENST00000620660.4	c.916A>G	p.Ile306Val	missense_variant	Exon 8 of 15	1		ENSP00000478721.1
RYK	ENST00000480381.1	n.276A>G		non_coding_transcript_exon_variant	Exon 2 of 4	5
RYK	ENST00000486725.1	n.-42A>G		upstream_gene_variant		2		ENSP00000417836.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Oct 30, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.916A>G (p.I306V) alteration is located in exon 8 (coding exon 8) of the RYK gene. This alteration results from a A to G substitution at nucleotide position 916, causing the isoleucine (I) at amino acid position 306 to be replaced by a valine (V). 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	0.27
BayesDel_addAF	Benign	-0.068	T
BayesDel_noAF	Benign	-0.33
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.12	T;.;.
Eigen	Uncertain	0.30
Eigen_PC	Uncertain	0.43
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.93	D;D;D
M_CAP	Benign	0.0090	T
MetaRNN	Benign	0.27	T;T;T
MetaSVM	Benign	-0.51	T
PrimateAI	Uncertain	0.64	T
PROVEAN	Benign	-0.10	N;.;.
Sift	Benign	0.48	T;.;.
Sift4G	Benign	0.59	T;T;T
Vest4		0.49, 0.48
MVP		0.24
ClinPred		0.62	D
GERP RS		6.0
Varity_R		0.16
gMVP		0.20

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: chr3-133910801;