NM_015693.4:c.1063G>A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_015693.4(INTU):c.1063G>A(p.Glu355Lys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
INTU
NM_015693.4 missense
NM_015693.4 missense
Scores
1
9
8
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.03
Publications
0 publications found
Genes affected
INTU (HGNC:29239): (inturned planar cell polarity protein) Involved in embryonic digit morphogenesis; roof of mouth development; and tongue morphogenesis. Located in ciliary basal body and motile cilium. Implicated in asphyxiating thoracic dystrophy and orofaciodigital syndrome XVII. [provided by Alliance of Genome Resources, Apr 2022]
INTU Gene-Disease associations (from GenCC):
- INTU-related skeletal ciliopathyInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
- orofaciodigital syndrome 17Inheritance: AR, Unknown Classification: MODERATE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
- short-rib thoracic dysplasia 20 with polydactylyInheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_015693.4. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| INTU | TSL:1 MANE Select | c.1063G>A | p.Glu355Lys | missense | Exon 5 of 16 | ENSP00000334003.5 | Q9ULD6-1 | ||
| INTU | TSL:1 | n.1063G>A | non_coding_transcript_exon | Exon 5 of 17 | ENSP00000421995.1 | Q9ULD6-3 | |||
| INTU | c.1063G>A | p.Glu355Lys | missense | Exon 5 of 16 | ENSP00000587218.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1386488Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 689844
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1386488
Hom.:
Cov.:
23
AF XY:
AC XY:
0
AN XY:
689844
African (AFR)
AF:
AC:
0
AN:
31106
American (AMR)
AF:
AC:
0
AN:
39908
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24668
East Asian (EAS)
AF:
AC:
0
AN:
37054
South Asian (SAS)
AF:
AC:
0
AN:
76274
European-Finnish (FIN)
AF:
AC:
0
AN:
51606
Middle Eastern (MID)
AF:
AC:
0
AN:
5364
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1063628
Other (OTH)
AF:
AC:
0
AN:
56880
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Uncertain
D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
P
Vest4
MutPred
Gain of ubiquitination at E355 (P = 0.0138)
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
Publications
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