chrX-50596772-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_020717.5(SHROOM4):​c.4405G>A​(p.Glu1469Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000107 in 1,210,509 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 8 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0000089 ( 0 hom., 1 hem., cov: 24)
Exomes 𝑓: 0.000011 ( 0 hom. 7 hem. )

Consequence

SHROOM4
NM_020717.5 missense

Scores

4
9
4

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.74
Variant links:
Genes affected
SHROOM4 (HGNC:29215): (shroom family member 4) This gene encodes a member of the APX/Shroom family, which contain an N-terminal PDZ domain and a C-terminal ASD2 motif. The encoded protein may play a role in cytoskeletal architecture. Mutations in this gene have been linked to the X-linked Stocco dos Santos syndrome characterized by cognitive disabilities. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jul 2017]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High Hemizygotes in GnomAdExome4 at 7 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SHROOM4NM_020717.5 linkc.4405G>A p.Glu1469Lys missense_variant Exon 9 of 9 ENST00000376020.9 NP_065768.2 Q9ULL8-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SHROOM4ENST00000376020.9 linkc.4405G>A p.Glu1469Lys missense_variant Exon 9 of 9 2 NM_020717.5 ENSP00000365188.2 Q9ULL8-1
SHROOM4ENST00000289292.11 linkc.4405G>A p.Glu1469Lys missense_variant Exon 9 of 10 1 ENSP00000289292.7 Q9ULL8-1
SHROOM4ENST00000460112.3 linkc.4057G>A p.Glu1353Lys missense_variant Exon 8 of 8 5 ENSP00000421450.1 Q9ULL8-2

Frequencies

GnomAD3 genomes
AF:
0.00000888
AC:
1
AN:
112556
Hom.:
0
Cov.:
24
AF XY:
0.0000288
AC XY:
1
AN XY:
34708
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000188
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000547
AC:
1
AN:
182950
Hom.:
0
AF XY:
0.0000148
AC XY:
1
AN XY:
67428
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000122
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000109
AC:
12
AN:
1097953
Hom.:
0
Cov.:
31
AF XY:
0.0000193
AC XY:
7
AN XY:
363323
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:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000131
Gnomad4 OTH exome
AF:
0.0000217
GnomAD4 genome
AF:
0.00000888
AC:
1
AN:
112556
Hom.:
0
Cov.:
24
AF XY:
0.0000288
AC XY:
1
AN XY:
34708
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000188
Gnomad4 OTH
AF:
0.00

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Sep 04, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.4405G>A (p.E1469K) alteration is located in exon 9 (coding exon 9) of the SHROOM4 gene. This alteration results from a G to A substitution at nucleotide position 4405, causing the glutamic acid (E) at amino acid position 1469 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
Pathogenic
0.60
BayesDel_addAF
Uncertain
0.017
T
BayesDel_noAF
Benign
-0.21
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Benign
0.12
T;T;.
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Pathogenic
0.98
D;.;D
M_CAP
Pathogenic
0.82
D
MetaRNN
Uncertain
0.60
D;D;D
MetaSVM
Benign
-0.59
T
MutationAssessor
Uncertain
2.5
M;M;.
PrimateAI
Uncertain
0.68
T
PROVEAN
Uncertain
-3.7
D;D;D
REVEL
Uncertain
0.38
Sift
Uncertain
0.0020
D;D;D
Sift4G
Uncertain
0.0090
D;D;D
Polyphen
1.0
D;D;.
Vest4
0.26
MutPred
0.68
Gain of ubiquitination at E1469 (P = 0.023);Gain of ubiquitination at E1469 (P = 0.023);.;
MVP
0.24
MPC
0.14
ClinPred
0.91
D
GERP RS
6.0
Varity_R
0.86
gMVP
0.55

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: rs1557246755; hg19: chrX-50339772; API