rs200076351

Variant summary

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

The NM_016946.6(F11R):​c.190T>C​(p.Phe64Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,894 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. F64I) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 31)
Exomes š‘“: 6.8e-7 ( 0 hom. )

Consequence

F11R
NM_016946.6 missense

Scores

2
7
10

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.54
Variant links:
Genes affected
F11R (HGNC:14685): (F11 receptor) Tight junctions represent one mode of cell-to-cell adhesion in epithelial or endothelial cell sheets, forming continuous seals around cells and serving as a physical barrier to prevent solutes and water from passing freely through the paracellular space. The protein encoded by this immunoglobulin superfamily gene member is an important regulator of tight junction assembly in epithelia. In addition, the encoded protein can act as (1) a receptor for reovirus, (2) a ligand for the integrin LFA1, involved in leukocyte transmigration, and (3) a platelet receptor. Multiple 5' alternatively spliced variants, encoding the same protein, have been identified but their biological validity has not been established. [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 rank MANE Protein UniProt
F11RNM_016946.6 linkc.190T>C p.Phe64Leu missense_variant Exon 3 of 10 ENST00000368026.11 NP_058642.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
F11RENST00000368026.11 linkc.190T>C p.Phe64Leu missense_variant Exon 3 of 10 1 NM_016946.6 ENSP00000357005.5 Q9Y624-1
ENSG00000270149ENST00000289779.7 linkn.*231T>C non_coding_transcript_exon_variant Exon 6 of 13 2 ENSP00000289779.4 A0A0A0MQY5
ENSG00000270149ENST00000289779.7 linkn.*231T>C 3_prime_UTR_variant Exon 6 of 13 2 ENSP00000289779.4 A0A0A0MQY5

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461894
Hom.:
0
Cov.:
32
AF XY:
0.00000138
AC XY:
1
AN XY:
727248
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:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.96
BayesDel_addAF
Uncertain
0.018
T
BayesDel_noAF
Benign
-0.21
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Benign
0.15
T;.
Eigen
Benign
0.17
Eigen_PC
Benign
0.19
FATHMM_MKL
Uncertain
0.93
D
LIST_S2
Benign
0.79
T;T
M_CAP
Benign
0.027
D
MetaRNN
Uncertain
0.66
D;D
MetaSVM
Benign
-0.68
T
MutationAssessor
Benign
1.6
L;L
PrimateAI
Uncertain
0.66
T
PROVEAN
Uncertain
-2.8
D;D
REVEL
Benign
0.27
Sift
Uncertain
0.029
D;T
Sift4G
Pathogenic
0.0
D;T
Polyphen
0.91
P;.
Vest4
0.66
MutPred
0.52
Loss of methylation at K63 (P = 0.0273);Loss of methylation at K63 (P = 0.0273);
MVP
0.68
MPC
0.82
ClinPred
0.96
D
GERP RS
4.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.75
gMVP
0.83

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: chr1-160970861; API