rs1553368900

chr2-50925809-ACACAATCCAGAAACCAACAAATGTTCAGAAAGAAGTTCAACTTACCATCTAACTTCAAGATGTACCCTATTAGTACTAAGAAATAAAGGACAAATGAGAGTTGGAAAAATAAGGTAGAAAGCACCCACCTTCCACATTGTTGTCTTCTGAAAGCACATGACAAGGAGGGAGAGAAAAGGAAAAACATTCATTAAGCAGCATGCAGACTGGACCTTGCCTTTGCATGTCTTCCTCATGCAAGGCACCAAACACATCATGCAAGTGCTCCATCACTATCATTCAAGGGGGAAAACAAAATCACAGGGAAGCAGGTTCCCTCCCATTGGCAGCATTGATAGGAAGTGAGACAAACTTTCATAATACTGCCATGCCCTGTGCAAAGAGTTTTTAAAAAAATCTTTCAACTACCCAGTATAAAGCAAACATTATTGTTATTACATGTTGCTGGTG-A

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_Moderate PM2 PP5_Moderate

The NM_001330078.2(NRXN1):c.773-304_790+128del variant causes a splice acceptor, splice donor, splice donor 5th base, coding sequence, intron change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: NRXN1 NM_001330078.2 splice_acceptor, splice_donor, splice_donor_5th_base, coding_sequence, intron
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 3.97

Genes affected

NRXN1 (HGNC:8008): (neurexin 1) This gene encodes a single-pass type I membrane protein that belongs to the neurexin family. Neurexins are cell-surface receptors that bind neuroligins to form Ca(2+)-dependent neurexin/neuroligin complexes at synapses in the central nervous system. This complex is required for efficient neurotransmission and is involved in the formation of synaptic contacts. Three members of this gene family have been studied in detail and are estimated to generate over 3,000 variants through the use of two alternative promoters (alpha and beta) and extensive alternative splicing in each family member. Recently, a third promoter (gamma) was identified for this gene in the 3' region. Mutations in this gene are associated with Pitt-Hopkins-like syndrome-2 and may contribute to susceptibility to schizophrenia. [provided by RefSeq, Aug 2016]

ACMG classification

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

• PVS1: Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 0.0037577364 fraction of the gene. No cryptic splice site detected. Exon removal is inframe change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 2-50925809-ACACAATCCAGAAACCAACAAATGTTCAGAAAGAAGTTCAACTTACCATCTAACTTCAAGATGTACCCTATTAGTACTAAGAAATAAAGGACAAATGAGAGTTGGAAAAATAAGGTAGAAAGCACCCACCTTCCACATTGTTGTCTTCTGAAAGCACATGACAAGGAGGGAGAGAAAAGGAAAAACATTCATTAAGCAGCATGCAGACTGGACCTTGCCTTTGCATGTCTTCCTCATGCAAGGCACCAAACACATCATGCAAGTGCTCCATCACTATCATTCAAGGGGGAAAACAAAATCACAGGGAAGCAGGTTCCCTCCCATTGGCAGCATTGATAGGAAGTGAGACAAACTTTCATAATACTGCCATGCCCTGTGCAAAGAGTTTTTAAAAAAATCTTTCAACTACCCAGTATAAAGCAAACATTATTGTTATTACATGTTGCTGGTG-A is Pathogenic according to our data. Variant chr2-50925809-ACACAATCCAGAAACCAACAAATGTTCAGAAAGAAGTTCAACTTACCATCTAACTTCAAGATGTACCCTATTAGTACTAAGAAATAAAGGACAAATGAGAGTTGGAAAAATAAGGTAGAAAGCACCCACCTTCCACATTGTTGTCTTCTGAAAGCACATGACAAGGAGGGAGAGAAAAGGAAAAACATTCATTAAGCAGCATGCAGACTGGACCTTGCCTTTGCATGTCTTCCTCATGCAAGGCACCAAACACATCATGCAAGTGCTCCATCACTATCATTCAAGGGGGAAAACAAAATCACAGGGAAGCAGGTTCCCTCCCATTGGCAGCATTGATAGGAAGTGAGACAAACTTTCATAATACTGCCATGCCCTGTGCAAAGAGTTTTTAAAAAAATCTTTCAACTACCCAGTATAAAGCAAACATTATTGTTATTACATGTTGCTGGTG-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 560109.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NRXN1	NM_001330078.2	c.773-304_790+128del		splice_acceptor_variant, splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant	3/23	ENST00000401669.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NRXN1	ENST00000401669.7	c.773-304_790+128del		splice_acceptor_variant, splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant	3/23	5	NM_001330078.2	A1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

provider interpretation

Geisinger Autism and Developmental Medicine Institute, Geisinger Health System

Jul 28, 2017

This 0.4 kilobase deletion was identified in a patient with autism spectrum disorder. The deletion includes exon 4 of the NRXN1 gene. Variants in the NRXN1 gene, including intragenic copy number variants, have been associated with variable neurodevelopmental diagnoses including autism spectrum disorders, intellectual disability, epilepsy, and schizophrenia. The features are variable from individual to individual. 2p16.3 deletions and variants in the NRXN1 gene have also been reported in healthy controls and unaffected parents of individuals with neuropsychiatric disorders indicating reduced penetrance or variable expressivity (Schaaf et al. 2012; Bena et al. 2013). -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1553368900; hg19: chr2-51152947;