chr2-157427380-C-T
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004288.5(CYTIP):c.517G>A(p.Glu173Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000028 in 1,609,842 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000072 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000023 ( 0 hom. )
Consequence
CYTIP
NM_004288.5 missense
NM_004288.5 missense
Scores
4
8
7
Clinical Significance
Conservation
PhyloP100: 3.63
Genes affected
CYTIP (HGNC:9506): (cytohesin 1 interacting protein) The protein encoded by this gene contains 2 leucine zipper domains and a putative C-terminal nuclear targeting signal, but does not have any hydrophobic regions. This protein is expressed weakly in resting NK and T cells. The encoded protein modulates the activation of ARF genes by CYTH1. This protein interacts with CYTH1 and SNX27 proteins and may act to sequester CYTH1 protein in the cytoplasm.[provided by RefSeq, Aug 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
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=0.21995077).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYTIP | NM_004288.5 | c.517G>A | p.Glu173Lys | missense_variant | 6/8 | ENST00000264192.8 | |
CYTIP | XM_017005386.3 | c.199G>A | p.Glu67Lys | missense_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYTIP | ENST00000264192.8 | c.517G>A | p.Glu173Lys | missense_variant | 6/8 | 1 | NM_004288.5 | P1 | |
CYTIP | ENST00000418920.5 | c.199G>A | p.Glu67Lys | missense_variant | 7/9 | 5 | |||
CYTIP | ENST00000457793.6 | c.*412G>A | 3_prime_UTR_variant, NMD_transcript_variant | 7/9 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152052Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
11
AN:
152052
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000118 AC: 29AN: 245934Hom.: 0 AF XY: 0.0000827 AC XY: 11AN XY: 133022
GnomAD3 exomes
AF:
AC:
29
AN:
245934
Hom.:
AF XY:
AC XY:
11
AN XY:
133022
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1457790Hom.: 0 Cov.: 30 AF XY: 0.0000221 AC XY: 16AN XY: 725026
GnomAD4 exome
AF:
AC:
34
AN:
1457790
Hom.:
Cov.:
30
AF XY:
AC XY:
16
AN XY:
725026
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152052Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74266
GnomAD4 genome
AF:
AC:
11
AN:
152052
Hom.:
Cov.:
32
AF XY:
AC XY:
10
AN XY:
74266
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Bravo
AF:
ExAC
AF:
AC:
7
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 submitter | clinical testing | Ambry Genetics | Nov 09, 2021 | The c.517G>A (p.E173K) alteration is located in exon 6 (coding exon 6) of the CYTIP gene. This alteration results from a G to A substitution at nucleotide position 517, causing the glutamic acid (E) at amino acid position 173 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Pathogenic
D;T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;N
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
D;.
Vest4
MutPred
Gain of MoRF binding (P = 0.0029);.;
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at