1-186406208-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_017847.6(ODR4):​c.1126G>A​(p.Glu376Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000601 in 1,611,400 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00058 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00060 ( 1 hom. )

Consequence

ODR4
NM_017847.6 missense

Scores

4
8
6

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.74
Variant links:
Genes affected
ODR4 (HGNC:24299): (odr-4 GPCR localization factor homolog) Predicted to be involved in protein localization. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=0.20984805).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ODR4NM_017847.6 linkuse as main transcriptc.1126G>A p.Glu376Lys missense_variant 12/14 ENST00000287859.11 NP_060317.3 Q5SWX8-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ODR4ENST00000287859.11 linkuse as main transcriptc.1126G>A p.Glu376Lys missense_variant 12/141 NM_017847.6 ENSP00000287859.6 Q5SWX8-1
ODR4ENST00000367470.8 linkuse as main transcriptc.1057G>A p.Glu353Lys missense_variant 11/135 ENSP00000356440.3 Q5SWX8-2
ODR4ENST00000419367.8 linkuse as main transcriptc.1030G>A p.Glu344Lys missense_variant 11/132 ENSP00000395084.3 Q5SWX8-4
ODR4ENST00000478571.1 linkuse as main transcriptn.239G>A non_coding_transcript_exon_variant 3/45

Frequencies

GnomAD3 genomes
AF:
0.000578
AC:
88
AN:
152152
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000145
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000393
Gnomad ASJ
AF:
0.00346
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000911
Gnomad OTH
AF:
0.000956
GnomAD3 exomes
AF:
0.000587
AC:
145
AN:
246878
Hom.:
0
AF XY:
0.000612
AC XY:
82
AN XY:
133974
show subpopulations
Gnomad AFR exome
AF:
0.000195
Gnomad AMR exome
AF:
0.000238
Gnomad ASJ exome
AF:
0.00309
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.0000465
Gnomad NFE exome
AF:
0.000872
Gnomad OTH exome
AF:
0.000673
GnomAD4 exome
AF:
0.000603
AC:
880
AN:
1459130
Hom.:
1
Cov.:
30
AF XY:
0.000599
AC XY:
435
AN XY:
725844
show subpopulations
Gnomad4 AFR exome
AF:
0.0000899
Gnomad4 AMR exome
AF:
0.000225
Gnomad4 ASJ exome
AF:
0.00276
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000375
Gnomad4 NFE exome
AF:
0.000681
Gnomad4 OTH exome
AF:
0.000597
GnomAD4 genome
AF:
0.000578
AC:
88
AN:
152270
Hom.:
0
Cov.:
32
AF XY:
0.000510
AC XY:
38
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.000144
Gnomad4 AMR
AF:
0.000392
Gnomad4 ASJ
AF:
0.00346
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000911
Gnomad4 OTH
AF:
0.000946
Alfa
AF:
0.000977
Hom.:
0
Bravo
AF:
0.000646
TwinsUK
AF:
0.000539
AC:
2
ALSPAC
AF:
0.000259
AC:
1
ESP6500AA
AF:
0.000270
AC:
1
ESP6500EA
AF:
0.000731
AC:
6
ExAC
AF:
0.000604
AC:
73
EpiCase
AF:
0.00121
EpiControl
AF:
0.00131

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 GeneticsJun 11, 2021The c.1126G>A (p.E376K) alteration is located in exon 12 (coding exon 11) of the C1orf27 gene. This alteration results from a G to A substitution at nucleotide position 1126, causing the glutamic acid (E) at amino acid position 376 to be replaced by a lysine (K). 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
0.48
BayesDel_addAF
Benign
-0.014
T
BayesDel_noAF
Uncertain
0.13
CADD
Pathogenic
27
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.27
.;.;T
Eigen
Pathogenic
0.74
Eigen_PC
Pathogenic
0.73
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Uncertain
0.91
D;D;D
M_CAP
Benign
0.026
D
MetaRNN
Benign
0.21
T;T;T
MetaSVM
Benign
-0.38
T
MutationAssessor
Uncertain
2.7
.;.;M
PROVEAN
Uncertain
-3.1
D;D;D
REVEL
Uncertain
0.34
Sift
Uncertain
0.0030
D;D;D
Sift4G
Uncertain
0.0090
D;D;D
Polyphen
1.0
.;D;D
Vest4
0.91
MVP
0.48
MPC
0.62
ClinPred
0.11
T
GERP RS
5.4
Varity_R
0.72
gMVP
0.71

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: rs201764660; hg19: chr1-186375340; API