X-41695641-G-A

Variant names:

• chrX-41695641-G-A
• NM_001097579.2:c.8G>A

Variant summary

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

The NM_001097579.2(GPR34):​c.8G>A​(p.Ser3Asn) 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. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 23)
• Consequence: GPR34 NM_001097579.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.13

Genes affected

GPR34 (HGNC:4490): (G protein-coupled receptor 34) G protein-coupled receptors (GPCRs), such as GPR34, are integral membrane proteins containing 7 putative transmembrane domains (TMs). These proteins mediate signals to the interior of the cell via activation of heterotrimeric G proteins that in turn activate various effector proteins, ultimately resulting in a physiologic response.[supplied by OMIM, Apr 2006]

CASK (HGNC:1497): (calcium/calmodulin dependent serine protein kinase) This gene encodes a calcium/calmodulin-dependent serine protein kinase. The encoded protein is a MAGUK (membrane-associated guanylate kinase) protein family member. These proteins are scaffold proteins and the encoded protein is located at synapses in the brain. Mutations in this gene are associated with FG syndrome 4, intellectual disability and microcephaly with pontine and cerebellar hypoplasia, and a form of X-linked intellectual disability. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]

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=0.14671302).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPR34	NM_001097579.2	c.8G>A	p.Ser3Asn	missense_variant	Exon 3 of 3	ENST00000378142.9	NP_001091048.1
CASK	NM_001367721.1	c.430-24111C>T		intron_variant	Intron 5 of 26	ENST00000378163.7	NP_001354650.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR34	ENST00000378142.9	c.8G>A	p.Ser3Asn	missense_variant	Exon 3 of 3	1	NM_001097579.2	ENSP00000367384.4
CASK	ENST00000378163.7	c.430-24111C>T		intron_variant	Intron 5 of 26	5	NM_001367721.1	ENSP00000367405.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 23

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Dec 26, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.8G>A (p.S3N) alteration is located in exon 3 (coding exon 1) of the GPR34 gene. This alteration results from a G to A substitution at nucleotide position 8, causing the serine (S) at amino acid position 3 to be replaced by an asparagine (N). 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	0.10
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	7.8
DANN	Benign	0.95
DEOGEN2	Benign	0.054	T;T;T
FATHMM_MKL	Benign	0.50	D
LIST_S2	Benign	0.39	.;.;T
M_CAP	Pathogenic	0.73	D
MetaRNN	Benign	0.15	T;T;T
MetaSVM	Benign	-0.75	T
MutationAssessor	Benign	1.4	L;L;L
PrimateAI	Benign	0.37	T
PROVEAN	Benign	-0.33	N;N;.
REVEL	Benign	0.16
Sift	Uncertain	0.022	D;D;.
Sift4G	Benign	0.11	T;T;.
Polyphen		0.024	B;B;B
Vest4		0.086
MutPred		0.17		Loss of glycosylation at S3 (P = 0.0158);Loss of glycosylation at S3 (P = 0.0158);Loss of glycosylation at S3 (P = 0.0158);
MVP		0.75
MPC		0.72
ClinPred		0.059	T
GERP RS		4.9
Varity_R		0.15
gMVP		0.28

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: chrX-41554894;