chrX-10523193-C-CAAAA

Variant names:

• chrX-10523193-C-CAAAA
• rs375668839
• NM_000381.4:c.661-10_661-7dupTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_000381.4(MID1):​c.661-10_661-7dupTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000022 (0 hom., 1 hem., cov: 19)
  • Exomes 𝑓: 0.000047 (0 hom. 0 hem.)
• Consequence: MID1 NM_000381.4 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 3 publications found

Genes affected

MID1 (HGNC:7095): (midline 1) The protein encoded by this gene is a member of the tripartite motif (TRIM) family, also known as the 'RING-B box-coiled coil' (RBCC) subgroup of RING finger proteins. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This protein forms homodimers which associate with microtubules in the cytoplasm. The protein is likely involved in the formation of multiprotein structures acting as anchor points to microtubules. Mutations in this gene have been associated with the X-linked form of Opitz syndrome, which is characterized by midline abnormalities such as cleft lip, laryngeal cleft, heart defects, hypospadias, and agenesis of the corpus callosum. This gene was also the first example of a gene subject to X inactivation in human while escaping it in mouse. Alternative promoter use, alternative splicing and alternative polyadenylation result in multiple transcript variants that have different tissue specificities. [provided by RefSeq, Dec 2016]

MID1 Gene-Disease associations (from GenCC):

• X-linked Opitz G/BBB syndrome

  Inheritance: XL Classification: DEFINITIVE, STRONG Submitted by: ClinGen, G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000381.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MID1	NM_000381.4	MANE Select	c.661-10_661-7dupTTTT		splice_region intron	N/A	NP_000372.1
	MID1	NM_001098624.2		c.661-10_661-7dupTTTT		splice_region intron	N/A	NP_001092094.1
	MID1	NM_001193277.1		c.661-10_661-7dupTTTT		splice_region intron	N/A	NP_001180206.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MID1	ENST00000317552.9	TSL:1 MANE Select	c.661-7_661-6insTTTT		splice_region intron	N/A	ENSP00000312678.4
	MID1	ENST00000380779.5	TSL:1	c.661-7_661-6insTTTT		splice_region intron	N/A	ENSP00000370156.1
	MID1	ENST00000380780.5	TSL:1	c.661-7_661-6insTTTT		splice_region intron	N/A	ENSP00000370157.1

Frequencies

GnomAD3 genomes AF: 0.0000220 AC: 1 AN: 45445 Hom.: 0 Cov.: 19

Gnomad AFR AF: 0.0000651

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000472 AC: 35 AN: 740833 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 206175

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000815 AC: 14 AN: 17181

American (AMR) AF: 0.000137 AC: 3 AN: 21884

Ashkenazi Jewish (ASJ) AF: 0.0000678 AC: 1 AN: 14745

East Asian (EAS) AF: 0.0000401 AC: 1 AN: 24951

South Asian (SAS) AF: 0.0000544 AC: 2 AN: 36735

European-Finnish (FIN) AF: 0.0000372 AC: 1 AN: 26856

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2252

European-Non Finnish (NFE) AF: 0.0000213 AC: 12 AN: 562683

Other (OTH) AF: 0.0000298 AC: 1 AN: 33546

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.0000220 AC: 1 AN: 45445 Hom.: 0 Cov.: 19 AF XY: 0.000111 AC XY: 1 AN XY: 9019

African (AFR) AF: 0.0000651 AC: 1 AN: 15351

American (AMR) AF: 0.00 AC: 0 AN: 3450

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1063

East Asian (EAS) AF: 0.00 AC: 0 AN: 1285

South Asian (SAS) AF: 0.00 AC: 0 AN: 972

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1502

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 59

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 20938

Other (OTH) AF: 0.00 AC: 0 AN: 571

Alfa AF: 0.00 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs375668839; hg19: chrX-10491233;