NM_004780.3(TCEAL1):c.169del (p.Leu57fs) AND Neurodevelopmental disorder with gait disturbance, dysmorphic facies, and behavioral abnormalities, X-linked

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 12, 2023
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003152645.4

Allele description [Variation Report for NM_004780.3(TCEAL1):c.169del (p.Leu57fs)]

NM_004780.3(TCEAL1):c.169del (p.Leu57fs)

Gene:

TCEAL1:transcription elongation factor A like 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xq22.2

Genomic location:

Preferred name:

NM_004780.3(TCEAL1):c.169del (p.Leu57fs)

HGVS:

NC_000023.11:g.103630085del
NM_001006639.2:c.169del
NM_001006640.2:c.169del
NM_004780.3:c.169delMANE SELECT
NP_001006640.1:p.Leu57fs
NP_001006641.1:p.Leu57fs
NP_004771.2:p.Leu57fs
NC_000023.10:g.102885013del
NM_001006639.2:c.169delC

Nucleotide change:

1-BP DEL, 169C

Protein change:

L57fs

Links:

OMIM: 300237.0005; dbSNP: rs2147641837

NCBI 1000 Genomes Browser:

rs2147641837

Molecular consequence:

NM_001006639.2:c.169del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001006640.2:c.169del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004780.3:c.169del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Neurodevelopmental disorder with gait disturbance, dysmorphic facies, and behavioral abnormalities, X-linked (HIJRS)
Synonyms:: HIJAZI-REIS SYNDROME
Identifiers:: MONDO: MONDO:0859085; MedGen: C5774179; OMIM: 301094

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003841021	OMIM	no assertion criteria provided	Pathogenic (Sep 12, 2023)	germline	literature only	Hijazi, H., Reis, L. M., Pehlivan, D., Bernstein, J. A., Muriello, M., Syverson, E., Bonner, D., Estiar, M. A., Gan-Or, Z., Rouleau, G. A., Lyulcheva, E., Greenhalgh, L., and 26 others TCEAL1 loss-of-function results in an X-linked dominant neurodevelopmental syndrome and drives the neurological disease trait in Xq22.2 deletions. Am. J. Hum. Genet. 109: 2270-2282, 2022.

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003841021

OMIM

no assertion criteria provided

Pathogenic
(Sep 12, 2023)

germline

literature only

Hijazi, H., Reis, L. M., Pehlivan, D., Bernstein, J. A., Muriello, M., Syverson, E., Bonner, D., Estiar, M. A., Gan-Or, Z., Rouleau, G. A., Lyulcheva, E., Greenhalgh, L., and 26 others TCEAL1 loss-of-function results in an X-linked dominant neurodevelopmental syndrome and drives the neurological disease trait in Xq22.2 deletions. Am. J. Hum. Genet. 109: 2270-2282, 2022.

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Details of each submission

From OMIM, SCV003841021.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	not provided

Description

In a 6-year-old girl (individual 7) with Hijazi-Reis syndrome (HIJRS; 301094), Hijazi et al. (2022) identified a de novo heterozygous 1-bp deletion (c.169delC, NM_001006639.2) in exon 3 of the TCEAL1 gene, predicted to result in a frameshift and premature termination (Leu57SerfsTer36). The mutation was found by exome sequencing. Functional studies of the variant and studies of patient cells were not performed.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 24, 2023

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