rs758534859

Variant names:

• chr19-35487460-C-A
• rs758534859
• NM_207392.3:c.268G>T

Your query was ambiguous. Multiple possible variants found:

• chr19-35487460-C-A
• chr19-35487460-C-T

Variant summary

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

The NM_207392.3(KRTDAP):​c.268G>T​(p.Gly90*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: KRTDAP NM_207392.3 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.57

Genes affected

KRTDAP (HGNC:16313): (keratinocyte differentiation associated protein) This gene encodes a protein which may function in the regulation of keratinocyte differentiation and maintenance of stratified epithelia. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

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
KRTDAP	NM_207392.3	c.268G>T	p.Gly90*	stop_gained	Exon 6 of 6	ENST00000338897.4	NP_997275.1
KRTDAP	NM_001244847.2	c.226G>T	p.Gly76*	stop_gained	Exon 5 of 5		NP_001231776.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KRTDAP	ENST00000338897.4	c.268G>T	p.Gly90*	stop_gained	Exon 6 of 6	1	NM_207392.3	ENSP00000339251.3
KRTDAP	ENST00000484218.6	c.226G>T	p.Gly76*	stop_gained	Exon 5 of 5	2		ENSP00000470713.1
KRTDAP	ENST00000479340.1	n.349G>T		non_coding_transcript_exon_variant	Exon 6 of 6	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.51	D
BayesDel_noAF	Pathogenic	0.49
CADD	Pathogenic	39
DANN	Uncertain	0.97
Eigen	Uncertain	0.55
Eigen_PC	Uncertain	0.32
FATHMM_MKL	Uncertain	0.86	D
Vest4		0.36
GERP RS		3.6

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs758534859; hg19: chr19-35978362;