3-14170550-CCT-ACG

Variant names:

• chr3-14170550-CCT-ACG
• NM_004628.5:c.300-2_300delAGGinsCGT
• XPC p.Arg100Ser

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PVS1_Moderate

The NM_004628.5(XPC):​c.300-2_300delAGGinsCGT​(p.Arg100Ser) variant causes a splice acceptor, missense, splice region, intron change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. R100R) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: XPC NM_004628.5 splice_acceptor, missense, splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.99
• Publications: 0 publications found

Genes affected

XPC (HGNC:12816): (XPC complex subunit, DNA damage recognition and repair factor) The protein encoded by this gene is a key component of the XPC complex, which plays an important role in the early steps of global genome nucleotide excision repair (NER). The encoded protein is important for damage sensing and DNA binding, and shows a preference for single-stranded DNA. Mutations in this gene or some other NER components can result in Xeroderma pigmentosum, a rare autosomal recessive disorder characterized by increased sensitivity to sunlight with the development of carcinomas at an early age. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2017]

XPC Gene-Disease associations (from GenCC):

• xeroderma pigmentosum group C

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Myriad Women's Health, G2P, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
• xeroderma pigmentosum

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.040028337 fraction of the gene. Cryptic splice site detected, with MaxEntScore 3.2, offset of 12, new splice context is: ttacaccgtgactttccaAGtga. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004628.5. 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
	XPC	NM_004628.5	MANE Select	c.300-2_300delAGGinsCGT	p.Arg100Ser	splice_acceptor missense splice_region intron	N/A	NP_004619.3
	XPC	NM_001354726.2		c.-156-2_-156delAGGinsCGT		splice_region	Exon 3 of 15	NP_001341655.1
	XPC	NM_001354727.2		c.300-2_300delAGGinsCGT	p.Arg100Ser	splice_acceptor missense splice_region intron	N/A	NP_001341656.1	A0ABB0MVJ4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XPC	ENST00000285021.12	TSL:1 MANE Select	c.300-2_300delAGGinsCGT	p.Arg100Ser	splice_acceptor missense splice_region intron	N/A	ENSP00000285021.8	Q01831-1
	XPC	ENST00000476581.6	TSL:1	n.300-2_300delAGGinsCGT		splice_acceptor splice_region intron non_coding_transcript_exon	Exon 3 of 15	ENSP00000424548.1	Q01831-3
	XPC	ENST00000850575.1		c.300-2_300delAGGinsCGT	p.Arg100Ser	splice_acceptor missense splice_region intron	N/A	ENSP00000520865.1	A0ABB0MVJ4

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

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		4.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr3-14212050;