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GeneBe

9-136405164-A-G

Variant summary

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

The NM_001039707.2(ENTR1):c.932T>C(p.Ile311Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,676 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000034 ( 0 hom. )

Consequence

ENTR1
NM_001039707.2 missense

Scores

3
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.63
Variant links:
Genes affected
ENTR1 (HGNC:10667): (endosome associated trafficking regulator 1) Involved in several processes, including endocytic recycling; positive regulation of cilium assembly; and positive regulation of protein localization to cilium. Located in endosome; microtubule organizing center; and midbody. Colocalizes with retromer complex. [provided by Alliance of Genome Resources, Apr 2022]

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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=0.18847987).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ENTR1NM_001039707.2 linkuse as main transcriptc.932T>C p.Ile311Thr missense_variant 7/10 ENST00000357365.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENTR1ENST00000357365.8 linkuse as main transcriptc.932T>C p.Ile311Thr missense_variant 7/105 NM_001039707.2 A1Q96C92-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000342
AC:
5
AN:
1461676
Hom.:
0
Cov.:
31
AF XY:
0.00000413
AC XY:
3
AN XY:
727122
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.0000224
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:
0.00000270
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.0000151

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 GeneticsJan 26, 2023The c.932T>C (p.I311T) alteration is located in exon 7 (coding exon 7) of the SDCCAG3 gene. This alteration results from a T to C substitution at nucleotide position 932, causing the isoleucine (I) at amino acid position 311 to be replaced by a threonine (T). 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
0.24
BayesDel_addAF
Benign
-0.038
T
BayesDel_noAF
Benign
-0.29
Cadd
Benign
17
Dann
Benign
0.91
DEOGEN2
Benign
0.011
T;.;.
Eigen
Benign
-0.15
Eigen_PC
Benign
-0.22
FATHMM_MKL
Benign
0.54
D
LIST_S2
Uncertain
0.87
D;D;D
M_CAP
Benign
0.037
D
MetaRNN
Benign
0.19
T;T;T
MetaSVM
Benign
-0.94
T
MutationTaster
Benign
1.0
N;N;N
PrimateAI
Uncertain
0.61
T
PROVEAN
Benign
-0.98
N;N;N
REVEL
Benign
0.075
Sift
Benign
0.19
T;T;T
Sift4G
Uncertain
0.027
D;D;D
Polyphen
0.93
P;P;P
Vest4
0.40
MutPred
0.33
Loss of stability (P = 0.0184);.;.;
MVP
0.82
MPC
0.030
ClinPred
0.24
T
GERP RS
3.4
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0
Varity_R
0.043
gMVP
0.082

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

LitVar

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

Other links and lift over

dbSNP: rs1166476207; hg19: chr9-139299616; API