X-103630030-T-TTCGGAGGAGCAGTCC

Variant names:

• chrX-103630030-T-TTCGGAGGAGCAGTCC
• NM_004780.3:c.124_138dupCAGTCCTCGGAGGAG

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PM4

The NM_004780.3(TCEAL1):​c.124_138dupCAGTCCTCGGAGGAG​(p.Gln42_Glu46dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 23)
  • Exomes 𝑓: 9.1e-7 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: TCEAL1 NM_004780.3 conservative_inframe_insertion
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.60

Genes affected

TCEAL1 (HGNC:11616): (transcription elongation factor A like 1) This gene encodes a member of the transcription elongation factor A (SII)-like (TCEAL) gene family. Members of this family may function as nuclear phosphoproteins that modulate transcription in a promoter context-dependent manner. The encoded protein is similar to transcription elongation factor A/transcription factor SII and contains a zinc finger-like motif as well as a sequence related to the transcription factor SII Pol II-binding region. It may exert its effects via protein-protein interactions with other transcriptional regulators rather than via direct binding of DNA. Multiple family members are located on the X chromosome. Alternative splicing results in multiple transcript variants encoding a single isoform. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_004780.3.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCEAL1	NM_004780.3	c.124_138dupCAGTCCTCGGAGGAG	p.Gln42_Glu46dup	conservative_inframe_insertion	Exon 3 of 3	ENST00000372625.8	NP_004771.2
TCEAL1	NM_001006639.2	c.124_138dupCAGTCCTCGGAGGAG	p.Gln42_Glu46dup	conservative_inframe_insertion	Exon 3 of 3		NP_001006640.1
TCEAL1	NM_001006640.2	c.124_138dupCAGTCCTCGGAGGAG	p.Gln42_Glu46dup	conservative_inframe_insertion	Exon 3 of 3		NP_001006641.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCEAL1	ENST00000372625.8	c.124_138dupCAGTCCTCGGAGGAG	p.Gln42_Glu46dup	conservative_inframe_insertion	Exon 3 of 3	1	NM_004780.3	ENSP00000361708.3
TCEAL1	ENST00000372624.3	c.124_138dupCAGTCCTCGGAGGAG	p.Gln42_Glu46dup	conservative_inframe_insertion	Exon 3 of 3	1		ENSP00000361707.3
TCEAL1	ENST00000469820.1	n.589_603dupCAGTCCTCGGAGGAG		non_coding_transcript_exon_variant	Exon 2 of 2	1
TCEAL1	ENST00000372626.7	c.124_138dupCAGTCCTCGGAGGAG	p.Gln42_Glu46dup	conservative_inframe_insertion	Exon 3 of 3	2		ENSP00000361709.3

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 9.12e-7 AC: 1 AN: 1096422 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 362012

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: 0.00000119

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 23

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Neurodevelopmental disorder with gait disturbance, dysmorphic facies, and behavioral abnormalities, X-linked Uncertain:1

-

Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-102884958;