NM_001018111.3:c.89_90insGTCACC

Variant names:

• chr7-131556270-G-GGGTGAC
• NM_001018111.3:c.89_90insGTCACC

Variant summary

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

The NM_001018111.3(PODXL):​c.89_90insGTCACC​(p.Pro30_Ser31insSerPro) variant causes a disruptive inframe insertion 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: not found (cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PODXL NM_001018111.3 disruptive_inframe_insertion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516

Genes affected

PODXL (HGNC:9171): (podocalyxin like) This gene encodes a member of the sialomucin protein family. The encoded protein was originally identified as an important component of glomerular podocytes. Podocytes are highly differentiated epithelial cells with interdigitating foot processes covering the outer aspect of the glomerular basement membrane. Other biological activities of the encoded protein include: binding in a membrane protein complex with Na+/H+ exchanger regulatory factor to intracellular cytoskeletal elements, playing a role in hematopoetic cell differentiation, and being expressed in vascular endothelium cells and binding to L-selectin. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PODXL	NM_001018111.3	c.89_90insGTCACC	p.Pro30_Ser31insSerPro	disruptive_inframe_insertion	Exon 1 of 9	ENST00000378555.8	NP_001018121.1
PODXL	NM_005397.4	c.89_90insGTCACC	p.Pro30_Ser31insSerPro	disruptive_inframe_insertion	Exon 1 of 8		NP_005388.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PODXL	ENST00000378555.8	c.89_90insGTCACC	p.Pro30_Ser31insSerPro	disruptive_inframe_insertion	Exon 1 of 9	1	NM_001018111.3	ENSP00000367817.3
PODXL	ENST00000322985.9	c.89_90insGTCACC	p.Pro30_Ser31insSerPro	disruptive_inframe_insertion	Exon 1 of 8	1		ENSP00000319782.9
PODXL	ENST00000446198.5	n.89_90insGTCACC		non_coding_transcript_exon_variant	Exon 1 of 7	2		ENSP00000390152.1
PODXL	ENST00000465001.1	n.291+854_291+855insGTCACC		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1311416 Hom.: 0 Cov.: 8 AF XY: 0.00 AC XY: 0 AN XY: 644804

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: 0.00

Gnomad4 OTH exome AF: 0.00

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: chr7-131241029;