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Intellectual disability v4.120 SUPT16H Achchuthan Shanmugasundram Publications for gene: SUPT16H were set to 31924697; 36226587; 36255738
Intellectual disability v4.120 SUPT16H Achchuthan Shanmugasundram Publications for gene: SUPT16H were set to 31924697; 36226587; 36255738
Intellectual disability v4.119 SUPT16H Achchuthan Shanmugasundram Publications for gene: SUPT16H were set to 31924697; 36226587; 36255738
Intellectual disability v4.120 SUPT16H Achchuthan Shanmugasundram Publications for gene: SUPT16H were set to 31924697; 36226587; 36255738
Intellectual disability v4.119 SUPT16H Achchuthan Shanmugasundram Publications for gene: SUPT16H were set to 31924697; 36226587; 36255738
Intellectual disability v4.119 SUPT16H Achchuthan Shanmugasundram Publications for gene: SUPT16H were set to 31924697; 36226587; 36255738
Intellectual disability v4.119 SUPT16H Achchuthan Shanmugasundram Publications for gene: SUPT16H were set to 31924697; 36226587; 36255738
Intellectual disability v4.119 SUPT16H Achchuthan Shanmugasundram Publications for gene: SUPT16H were set to 31924697; 36226587
Intellectual disability v4.114 SUPT16H Achchuthan Shanmugasundram Publications for gene: SUPT16H were set to 31924697; 36226587
Intellectual disability v4.113 SUPT16H Achchuthan Shanmugasundram Publications for gene: SUPT16H were set to 31924697; 36226587
Intellectual disability v4.114 SUPT16H Achchuthan Shanmugasundram Publications for gene: SUPT16H were set to 31924697; 36226587
Intellectual disability v4.114 SUPT16H Achchuthan Shanmugasundram Publications for gene: SUPT16H were set to 31924697; 36226587
Intellectual disability v4.114 SUPT16H Achchuthan Shanmugasundram Publications for gene: SUPT16H were set to 31924697; 36226587
Intellectual disability v4.114 SUPT16H Achchuthan Shanmugasundram Publications for gene: SUPT16H were set to 31924697; 36226587
Intellectual disability v4.113 SUPT16H Achchuthan Shanmugasundram Publications for gene: SUPT16H were set to 31924697; 36226587
Intellectual disability v4.112 SUPT16H Achchuthan Shanmugasundram Phenotypes for gene: SUPT16H were changed from Neurodevelopmental disorder with dysmorphic facies and thin corpus callosum, OMIM:619480; Global developmental delay; Intellectual disability; Abnormality of the corpus callosum to Neurodevelopmental disorder with dysmorphic facies and thin corpus callosum, OMIM:619480; Global developmental delay; Intellectual disability; Abnormality of the corpus callosum
Intellectual disability v4.113 SUPT16H Achchuthan Shanmugasundram Publications for gene: SUPT16H were set to 31924697
Intellectual disability v4.112 SUPT16H Achchuthan Shanmugasundram Phenotypes for gene: SUPT16H were changed from Neurodevelopmental disorder with dysmorphic facies and thin corpus callosum, OMIM:619480; Global developmental delay; Intellectual disability; Abnormality of the corpus callosum to Neurodevelopmental disorder with dysmorphic facies and thin corpus callosum, OMIM:619480; Global developmental delay; Intellectual disability; Abnormality of the corpus callosum
Intellectual disability v4.112 SUPT16H Achchuthan Shanmugasundram Phenotypes for gene: SUPT16H were changed from Neurodevelopmental disorder with dysmorphic facies and thin corpus callosum, OMIM:619480; Global developmental delay; Intellectual disability; Abnormality of the corpus callosum to Neurodevelopmental disorder with dysmorphic facies and thin corpus callosum, OMIM:619480; Global developmental delay; Intellectual disability; Abnormality of the corpus callosum
Intellectual disability v4.111 SUPT16H Achchuthan Shanmugasundram Phenotypes for gene: SUPT16H were changed from Neurodevelopmental disorder with dysmorphic facies and thin corpus callosum, OMIM:619480; Global developmental delay; Intellectual disability; Abnormality of the corpus callosum to Neurodevelopmental disorder with dysmorphic facies and thin corpus callosum, OMIM:619480; Global developmental delay; Intellectual disability; Abnormality of the corpus callosum
Intellectual disability v4.111 SUPT16H Achchuthan Shanmugasundram Phenotypes for gene: SUPT16H were changed from Neurodevelopmental disorder with dysmorphic facies and thin corpus callosum, OMIM:619480; Global developmental delay; Intellectual disability; Abnormality of the corpus callosum to Neurodevelopmental disorder with dysmorphic facies and thin corpus callosum, OMIM:619480; Global developmental delay; Intellectual disability; Abnormality of the corpus callosum
Intellectual disability v4.111 SUPT16H Achchuthan Shanmugasundram Phenotypes for gene: SUPT16H were changed from Neurodevelopmental disorder with dysmorphic facies and thin corpus callosum, OMIM:619480; Global developmental delay; Intellectual disability; Abnormality of the corpus callosum to Neurodevelopmental disorder with dysmorphic facies and thin corpus callosum, OMIM:619480; Global developmental delay; Intellectual disability; Abnormality of the corpus callosum
Intellectual disability v4.111 SUPT16H Achchuthan Shanmugasundram Phenotypes for gene: SUPT16H were changed from Global developmental delay; Intellectual disability; Abnormality of the corpus callosum to Neurodevelopmental disorder with dysmorphic facies and thin corpus callosum, OMIM:619480; Global developmental delay; Intellectual disability; Abnormality of the corpus callosum
Intellectual disability v3.1511 SUPT16H Arina Puzriakova Tag for-review was removed from gene: SUPT16H.
Intellectual disability v3.1510 SUPT16H Sarah Leigh commented on gene: SUPT16H
Intellectual disability v3.1509 SUPT16H Arina Puzriakova Source Expert Review Green was added to SUPT16H.
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
Intellectual disability v3.278 SUPT16H Arina Puzriakova Publications for gene: SUPT16H were set to http://dx.doi.org/10.1136/jmedgenet-2019-106193
Intellectual disability v3.277 SUPT16H Arina Puzriakova Classified gene: SUPT16H as Amber List (moderate evidence)
Intellectual disability v3.277 SUPT16H Arina Puzriakova Added comment: Comment on list classification: There is sufficient evidence for this gene to be rated GREEN at the next major review - at least four unrelated individuals with GDD/ID (plus another additional patient with a deletion, albeit encompassing other potentially clinically relevant genes).
Intellectual disability v3.277 SUPT16H Arina Puzriakova Gene: supt16h has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.276 SUPT16H Arina Puzriakova Tag for-review tag was added to gene: SUPT16H.
Intellectual disability v3.0 SUPT16H Konstantinos Varvagiannis gene: SUPT16H was added
gene: SUPT16H was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: SUPT16H was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: SUPT16H were set to http://dx.doi.org/10.1136/jmedgenet-2019-106193
Phenotypes for gene: SUPT16H were set to Global developmental delay; Intellectual disability; Abnormality of the corpus callosum
Penetrance for gene: SUPT16H were set to Complete
Review for gene: SUPT16H was set to AMBER
Added comment: Bina et al (2020 - http://dx.doi.org/10.1136/jmedgenet-2019-106193) report on 4 unrelated individuals with heterozygous SNVs affecting SUPT16H as well as 1 further with microdeletion spanning this gene.

The phenotype consisted of DD with subsequent ID in a subset of them (ages of the cohort: 2y-14y), autistic features in few, abnormalities of the corpus callosum (for 3 with available MRI images), variable gastrointestinal problems in some, and possibly minor dysmorphic features.

SUPT16H encodes a subunit of the FACT (facilitates chromatin transcription) complex, a chromatin-specific factor required for transcription elongation as well as for DNA replication and repair (OMIM citing Belotserkovskaya et al. 2003 - PMID: 12934006). The 2 subunits of the complex [Spt16 (encoded by SUPT16H) and SSRP1] are essential for histone regulation. As the authors note, Spt16 interacts with the histone dimer H2A-H2B during transcription to allow RNA polymerase access to previously coiled DNA [cited PMIDs : 9489704, 10421373 / A recent study by Liu et al 2019 (PMID: 31775157) appears highly relevant].

SUPT16H has a Z-score of 5.1 in gnomAD and a pLI of 1 (%HI of 22.56 in Decipher).

SNVs :
4 de novo missense SNVs were identified following exome sequencing (NM_007192.3:c.484A>G or I162V / L432P / N571S / R734W), all absent from gnomAD and mostly predicted to be deleterious (I162V predicted benign, tolerated, disease-causing by PolyPhen2, SIFT, MutationTaster respectively and had a CADD score of 13.61). Prior work-up for these individuals (incl. CMA in some / MS-MLPA for Angelman s. in 1 / metabolic investigations) had (probably) not revealed an apparent cause, with small CNVs inherited from healthy parents (a 4q13.3 dup / 20q13.2 del - coordinates not provided).

There were no studies performed for the identified variants.

CNVs :
A 5th individual reported by Bina et al was found to harbor a 2.05 Mb 14q11.2 deletion spanning SUPT16H. The specific deletion also spanned CHD8 while the same individual harbored also a 30.17 Mb duplication of 18p11.32q12.1.

CNVs spanning SUPT16H reported to date, also span the (very) proximal CHD8. [Genomic coordinates (GRCh38) for SUPT16H and CHD8 as provided by OMIM : 14:21,351,471-21,384,018 / 14:21,385,198-21,456,122]. Haploinsufficiency of CHD8 is associated with a distinctive syndrome with overgrowth and ID (Douzgou et al 2019 - PMID: 31001818). The phenotype of SUPT16H-CHD8 duplications is discussed in other studies/reviews. [Smol et al 2020 - PMID: 31823155 / Smyk et al 2016 - PMID: 26834018].

Animal models were not commented on by Bina et al (possibly not available for mouse : http://www.informatics.jax.org/marker/MGI:1890948 / https://www.mousephenotype.org/data/genes/MGI:1890948 ).
Sources: Literature