chrX-108614917-TTGGACCAAATGGACAACC-T

Position:

• chrX-108614917-TTGGACCAAATGGACAACC-T

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2 PM4 PP5

The NM_033380.3(COL4A5):​c.2411_2428del​(p.Asn804_Pro809del) variant causes a inframe deletion change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in Lovd as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 22)
• Consequence: COL4A5 NM_033380.3 inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.47

Genes affected

COL4A5 (HGNC:2207): (collagen type IV alpha 5 chain) This gene encodes one of the six subunits of type IV collagen, the major structural component of basement membranes. Mutations in this gene are associated with X-linked Alport syndrome, also known as hereditary nephritis. Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head conformation with another type IV collagen gene so that each gene pair shares a common promoter. Alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Aug 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_033380.3.
• PP5: Variant X-108614917-TTGGACCAAATGGACAACC-T is Pathogenic according to our data. Variant chrX-108614917-TTGGACCAAATGGACAACC-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL4A5	NM_033380.3	c.2411_2428del	p.Asn804_Pro809del	inframe_deletion	30/53	ENST00000328300.11	NP_203699.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL4A5	ENST00000328300.11	c.2411_2428del	p.Asn804_Pro809del	inframe_deletion	30/53	1	NM_033380.3	ENSP00000331902
COL4A5	ENST00000483338.1	c.1235_1252del	p.Asn412_Pro417del	inframe_deletion	14/20	1		ENSP00000495685
COL4A5	ENST00000361603.7	c.2411_2428del	p.Asn804_Pro809del	inframe_deletion	30/51	2		ENSP00000354505	P1

Frequencies

GnomAD3 genomes Cov.: 22

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

GnomAD4 genome Cov.: 22

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

LitVar

Other links and lift over

dbSNP: rs104886353; hg19: chrX-107858147;