chr3-52502014-G-A

Variant summary

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

The NM_015136.3(STAB1):​c.340G>A​(p.Gly114Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,460,222 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.000014 ( 0 hom. )

Consequence

STAB1
NM_015136.3 missense

Scores

4
13
2

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.48
Variant links:
Genes affected
STAB1 (HGNC:18628): (stabilin 1) This gene encodes a large, transmembrane receptor protein which may function in angiogenesis, lymphocyte homing, cell adhesion, or receptor scavenging. The protein contains 7 fasciclin, 16 epidermal growth factor (EGF)-like, and 2 laminin-type EGF-like domains as well as a C-type lectin-like hyaluronan-binding Link module. The protein is primarily expressed on sinusoidal endothelial cells of liver, spleen, and lymph node. The receptor has been shown to endocytose ligands such as low density lipoprotein, Gram-positive and Gram-negative bacteria, and advanced glycosylation end products. Supporting its possible role as a scavenger receptor, the protein rapidly cycles between the plasma membrane and early endosomes. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
STAB1NM_015136.3 linkuse as main transcriptc.340G>A p.Gly114Arg missense_variant 4/69 ENST00000321725.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
STAB1ENST00000321725.10 linkuse as main transcriptc.340G>A p.Gly114Arg missense_variant 4/691 NM_015136.3 P1Q9NY15-1
STAB1ENST00000481607.1 linkuse as main transcriptn.395G>A non_coding_transcript_exon_variant 4/211

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.0000137
AC:
20
AN:
1460222
Hom.:
0
Cov.:
32
AF XY:
0.0000165
AC XY:
12
AN XY:
726404
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000171
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000378

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJul 05, 2023The c.340G>A (p.G114R) alteration is located in exon 4 (coding exon 4) of the STAB1 gene. This alteration results from a G to A substitution at nucleotide position 340, causing the glycine (G) at amino acid position 114 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
Uncertain
0.41
BayesDel_addAF
Uncertain
0.15
D
BayesDel_noAF
Uncertain
-0.020
CADD
Uncertain
24
DANN
Pathogenic
1.0
DEOGEN2
Uncertain
0.60
D
Eigen
Uncertain
0.60
Eigen_PC
Uncertain
0.53
FATHMM_MKL
Uncertain
0.86
D
LIST_S2
Uncertain
0.93
D
M_CAP
Uncertain
0.15
D
MetaRNN
Uncertain
0.68
D
MetaSVM
Uncertain
0.68
D
MutationAssessor
Pathogenic
3.3
M
MutationTaster
Benign
0.65
N
PrimateAI
Benign
0.46
T
PROVEAN
Pathogenic
-6.7
D
REVEL
Uncertain
0.44
Sift
Uncertain
0.0010
D
Sift4G
Pathogenic
0.0
D
Polyphen
0.86
P
Vest4
0.53
MutPred
0.26
Loss of catalytic residue at G114 (P = 0.1039);
MVP
0.87
MPC
0.60
ClinPred
0.99
D
GERP RS
4.4
Varity_R
0.55
gMVP
0.85

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1234235491; hg19: chr3-52536030; API