X-50598527-A-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_020717.5(SHROOM4):c.3951T>A(p.Leu1317=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 22)
Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )
Failed GnomAD Quality Control
Consequence
SHROOM4
NM_020717.5 synonymous
NM_020717.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0300
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
Variant X-50598527-A-T is Benign according to our data. Variant chrX-50598527-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 3341975.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.03 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SHROOM4 | NM_020717.5 | c.3951T>A | p.Leu1317= | synonymous_variant | 8/9 | ENST00000376020.9 | NP_065768.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SHROOM4 | ENST00000376020.9 | c.3951T>A | p.Leu1317= | synonymous_variant | 8/9 | 2 | NM_020717.5 | ENSP00000365188 | P1 | |
SHROOM4 | ENST00000289292.11 | c.3951T>A | p.Leu1317= | synonymous_variant | 8/10 | 1 | ENSP00000289292 | P1 | ||
SHROOM4 | ENST00000460112.3 | c.3603T>A | p.Leu1201= | synonymous_variant | 7/8 | 5 | ENSP00000421450 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD3 genomes
Cov.:
22
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1091192Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 357678
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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0
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1091192
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31
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0
AN XY:
357678
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GnomAD4 genome Cov.: 22
GnomAD4 genome
Cov.:
22
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2024 | SHROOM4: PM2:Supporting, BP4, BP7 - |
Computational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.