chr2-10790777-T-G

Variant names:

• chr2-10790777-T-G
• rs4807
• NM_005742.4:c.641A>C

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_005742.4(PDIA6):​c.641A>C​(p.Lys214Thr) variant causes a missense change. 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: 33)
• Consequence: PDIA6 NM_005742.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.15
• Publications: 44 publications found

Genes affected

PDIA6 (HGNC:30168): (protein disulfide isomerase family A member 6) This gene encodes a member of the disulfide isomerase (PDI) family of endoplasmic reticulum (ER) proteins that catalyze protein folding and thiol-disulfide interchange reactions. The encoded protein has an N-terminal ER-signal sequence, two catalytically active thioredoxin (TRX) domains, a TRX-like domain, and a C-terminal ER-retention sequence. This protein inhibits the aggregation of misfolded proteins and exhibits both isomerase and chaperone activity. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2016]

ACMG classification

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

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005742.4. 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
	PDIA6	NM_005742.4	MANE Select	c.641A>C	p.Lys214Thr	missense	Exon 7 of 13	NP_005733.1	Q15084-1
	PDIA6	NM_001282704.2		c.797A>C	p.Lys266Thr	missense	Exon 9 of 15	NP_001269633.1	Q15084-2
	PDIA6	NM_001282705.2		c.785A>C	p.Lys262Thr	missense	Exon 8 of 14	NP_001269634.1	Q15084-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDIA6	ENST00000272227.8	TSL:1 MANE Select	c.641A>C	p.Lys214Thr	missense	Exon 7 of 13	ENSP00000272227.4	Q15084-1
	PDIA6	ENST00000404371.6	TSL:2	c.797A>C	p.Lys266Thr	missense	Exon 9 of 15	ENSP00000385385.2	Q15084-2
	PDIA6	ENST00000617249.4	TSL:5	c.797A>C	p.Lys266Thr	missense	Exon 8 of 14	ENSP00000481892.1	Q15084-2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.38
BayesDel_addAF	Uncertain	0.022	T
BayesDel_noAF	Benign	-0.21
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.12	T
Eigen	Uncertain	0.27
Eigen_PC	Uncertain	0.33
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.92	D
M_CAP	Benign	0.019	T
MetaRNN	Uncertain	0.55	D
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.6	L
PhyloP100		5.1
PrimateAI	Uncertain	0.62	T
PROVEAN	Pathogenic	-5.1	D
REVEL	Benign	0.19
Sift	Benign	0.046	D
Sift4G	Benign	0.088	T
Polyphen		0.83	P
Vest4		0.58
MutPred		0.47		Loss of ubiquitination at K214 (P = 0.021)
MVP		0.38
MPC		0.40
ClinPred		0.98	D
GERP RS		4.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.76
gMVP		0.85
Mutation Taster		=21/79	disease causing

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

Other links and lift over

dbSNP: rs4807; hg19: chr2-10930903;