rs58747104

Variant names:

• chr11-68903812-G-GCCGCCATCTTC
• NM_181514.2:c.-3_-2insGAAGATGGCGG

Your query was ambiguous. Multiple possible variants found:

• chr11-68903812-G-GCCGCCATCTTC
• chr11-68903812-G-GCCGCCGCCATCTTC
• chr11-68903812-G-GCCGCCGCGATCTTC
• chr11-68903812-G-GCCGCCGGCATCTTC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_181514.2(MRPL21):​c.-3_-2insGAAGATGGCGG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 0)
• Consequence: MRPL21 NM_181514.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

Genes affected

MRPL21 (HGNC:14479): (mitochondrial ribosomal protein L21) Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 39S subunit protein. Multiple transcript variants encoding different isoforms were identified through sequence analysis although some may be subject to nonsense-mediated decay (NMD). [provided by RefSeq, Jul 2008]

IGHMBP2 (HGNC:5542): (immunoglobulin mu DNA binding protein 2) This gene encodes a helicase superfamily member that binds a specific DNA sequence from the immunoglobulin mu chain switch region. Mutations in this gene lead to spinal muscle atrophy with respiratory distress type 1. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRPL21	NM_181514.2	c.-3_-2insGAAGATGGCGG		5_prime_UTR_variant	Exon 1 of 7	ENST00000362034.7	NP_852615.1
MRPL21	NM_181515.2	c.-271_-270insGAAGATGGCGG		5_prime_UTR_variant	Exon 1 of 7		NP_852616.1
MRPL21	XM_005273823.5	c.-3_-2insGAAGATGGCGG		5_prime_UTR_variant	Exon 1 of 6		XP_005273880.1
MRPL21	XR_247190.5	n.20_21insGAAGATGGCGG		non_coding_transcript_exon_variant	Exon 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRPL21	ENST00000362034.7	c.-3_-2insGAAGATGGCGG		5_prime_UTR_variant	Exon 1 of 7	1	NM_181514.2	ENSP00000354580.2

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 45

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

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: chr11-68671280;