NM_016648.4:c.503_504dupTT

Variant names:

• chr4-112646904-A-ATT
• rs1554011296
• NM_016648.4:c.503_504dupTT

Variant summary

Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_016648.4(LARP7):​c.503_504dupTT​(p.Ala169LeufsTer37) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: LARP7 NM_016648.4 frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: 7.33
• Publications: 1 publications found

Genes affected

LARP7 (HGNC:24912): (La ribonucleoprotein 7, transcriptional regulator) This gene encodes a protein which is found in the 7SK snRNP (small nuclear ribonucleoprotein). This snRNP complex inhibits a cyclin-dependent kinase, positive transcription elongation factor b, which is required for paused RNA polymerase II at a promoter to begin transcription elongation. A pseudogene of this gene is located on chromosome 3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2012]

MIR302CHG (HGNC:41070): (miR-302/367 cluster host gene)

ACMG classification

Our verdict: Pathogenic. The variant received 12 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 4-112646904-A-ATT is Pathogenic according to our data. Variant chr4-112646904-A-ATT is described in ClinVar as Pathogenic. ClinVar VariationId is 523643.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016648.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LARP7	NM_016648.4	MANE Select	c.503_504dupTT	p.Ala169LeufsTer37	frameshift	Exon 5 of 13	NP_057732.2
	LARP7	NM_001370974.1		c.503_504dupTT	p.Ala169LeufsTer37	frameshift	Exon 5 of 13	NP_001357903.1
	LARP7	NM_001370975.1		c.503_504dupTT	p.Ala169LeufsTer37	frameshift	Exon 5 of 13	NP_001357904.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LARP7	ENST00000344442.10	TSL:2 MANE Select	c.503_504dupTT	p.Ala169LeufsTer37	frameshift	Exon 5 of 13	ENSP00000344950.5
	LARP7	ENST00000509061.5	TSL:1	c.503_504dupTT	p.Ala169LeufsTer37	frameshift	Exon 7 of 15	ENSP00000422626.2
	LARP7	ENST00000509622.5	TSL:1	n.*262_*263dupTT		non_coding_transcript_exon	Exon 5 of 13	ENSP00000422451.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions as Germline

Significance: Pathogenic

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
2	-	-	Microcephalic primordial dwarfism, Alazami type (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.3
Mutation Taster		=0/200	disease causing (ClinVar)

Splicing

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

Other links and lift over

dbSNP: rs1554011296; hg19: chr4-113568060;