TCEAL1

transcription elongation factor A like 1, the group of Transcription elongation factor A like family

Basic information

Region (hg38): X:103628704-103630953

Links

ENSG00000172465 ∙ NCBI:9338 ∙ OMIM:300237 ∙ HGNC:11616 ∙ Uniprot:Q15170 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with gait disturbance, dysmorphic facies, and behavioral abnormalities, X-linked (Moderate), mode of inheritance: XL
• neurodevelopmental disorder with gait disturbance, dysmorphic facies, and behavioral abnormalities, X-linked (Strong), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hijazi-Reis syndrome (Neurodevelopmental disorder with gait disturbance, dysmorphic facies and behavioral abnormalities, X-linked)	XL	Allergy/Immunology/Infectious	In addition to other features, recurrent infections have been described (including respiratory and ear infections), and awareness may allow early and aggressive treatment of infections	Allergy/Immunology/Infectious; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	36368327

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TCEAL1 gene.

• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCEAL1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense		1	6	1		8
nonsense	1	4				5
start loss						0
frameshift		4	2			6
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	9	9	3	0

Variants in TCEAL1

This is a list of pathogenic ClinVar variants found in the TCEAL1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-103629922-C-T			Likely benign (Apr 01, 2023)
X-103629944-G-C		Inborn genetic diseases	Uncertain significance (Mar 08, 2024)
X-103629950-C-T		Inborn genetic diseases	Uncertain significance (Nov 18, 2023)
X-103629977-G-T		Neurodevelopmental disorder with gait disturbance, dysmorphic facies, and behavioral abnormalities, X-linked	Likely pathogenic (-)
X-103629999-C-CT		not specified	Uncertain significance (Jun 12, 2023)
X-103630004-G-GT		Neurodevelopmental disorder with gait disturbance, dysmorphic facies, and behavioral abnormalities, X-linked	Uncertain significance (Jan 09, 2024)
X-103630014-C-T		Inborn genetic diseases	Uncertain significance (Dec 03, 2021)
X-103630030-T-TTCGGAGGAGCAGTCC		Neurodevelopmental disorder with gait disturbance, dysmorphic facies, and behavioral abnormalities, X-linked	Uncertain significance (-)
X-103630064-C-T		Inborn genetic diseases	Uncertain significance (Jun 29, 2022)
X-103630067-G-T		Neurodevelopmental disorder with gait disturbance, dysmorphic facies, and behavioral abnormalities, X-linked	Likely pathogenic (-)
X-103630084-GC-G		See cases • Neurodevelopmental disorder with gait disturbance, dysmorphic facies, and behavioral abnormalities, X-linked	Likely pathogenic (Aug 02, 2022)
X-103630112-G-T		Inborn genetic diseases	Pathogenic (Oct 27, 2023)
X-103630175-C-T		See cases • Neurodevelopmental disorder with gait disturbance, dysmorphic facies, and behavioral abnormalities, X-linked	Likely pathogenic (Aug 02, 2022)
X-103630185-G-A		See cases • Neurodevelopmental disorder with gait disturbance, dysmorphic facies, and behavioral abnormalities, X-linked	Likely pathogenic (Aug 02, 2022)
X-103630192-A-G			Likely benign (Mar 01, 2022)
X-103630210-AGAAG-A		See cases • Neurodevelopmental disorder with gait disturbance, dysmorphic facies, and behavioral abnormalities, X-linked	Likely pathogenic (Aug 02, 2022)
X-103630222-TAAAG-T		Neurodevelopmental disorder with gait disturbance, dysmorphic facies, and behavioral abnormalities, X-linked	Likely pathogenic (-)
X-103630237-TCGTTCTCGCC-T		Neurodevelopmental disorder with gait disturbance, dysmorphic facies, and behavioral abnormalities, X-linked	Likely pathogenic (-)
X-103630262-G-A		See cases	Uncertain significance (Aug 02, 2022)
X-103630329-A-G		not specified	Likely benign (Dec 26, 2023)
X-103630343-A-C			Uncertain significance (Jun 01, 2024)
X-103630363-G-A		See cases • Neurodevelopmental disorder with gait disturbance, dysmorphic facies, and behavioral abnormalities, X-linked	Likely pathogenic (Aug 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCEAL1	protein_coding	protein_coding	ENST00000372625	1	2250

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.586	0.376	122593	1	0	122594	0.00000408

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	35	57.3	0.611	0.00000383	1056
Missense in Polyphen		12	17.187	0.69821		289
Synonymous	-0.0328	21	20.8	1.01	0.00000133	290
Loss of Function	1.53	0	2.73	0.00	1.72e-7	63

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000126	0.0000468
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation. Modulates various viral and cellular promoters in a promoter context- dependent manner. For example, transcription from the FOS promoter is increased, while Rous sarcoma virus (RSV) long terminal repeat (LTR) promoter activity is repressed. Does not bind DNA directly.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.43

Haploinsufficiency Scores

• pHI: 0.0528
• hipred: Y
• hipred_score: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.988

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tceal1

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm
• Molecular function: DNA-binding transcription factor activity;WW domain binding