11-82914827-C-G

Position:

• chr11-82914827-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_145018.4(DDIAS):​c.89C>G​(p.Ser30Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000277 in 1,442,678 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000028 (0 hom.)
• Consequence: DDIAS NM_145018.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.64

Genes affected

DDIAS (HGNC:26351): (DNA damage induced apoptosis suppressor) Involved in negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage and regulation of DNA stability. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

PRCP (HGNC:9344): (prolylcarboxypeptidase) This gene encodes a member of the peptidase S28 family of serine exopeptidases. The encoded preproprotein is proteolytically processed to generate the mature lysosomal prolylcarboxypeptidase. This enzyme cleaves C-terminal amino acids linked to proline in peptides such as angiotension II, III and des-Arg9-bradykinin. The cleavage occurs at acidic pH, but the enzyme activity is retained with some substrates at neutral pH. This enzyme has been shown to be an activator of the cell matrix-associated prekallikrein. The importance of angiotension II, one of the substrates of this enzyme, in regulating blood pressure and electrolyte balance suggests that this gene may be related to essential hypertension. A pseudogene of this gene has been identified on chromosome 2. Alternative splicing results in multiple transcript variants, at least one of which encodes an isoform that is proteolytically processed. [provided by RefSeq, Jan 2016]

DDIAS (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.38624522).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDIAS	NM_145018.4	c.89C>G	p.Ser30Cys	missense_variant	3/6	ENST00000533655.6	NP_659455.3
DDIAS	NM_001363481.2	c.89C>G	p.Ser30Cys	missense_variant	2/5		NP_001350410.1
DDIAS	XM_011544836.3	c.89C>G	p.Ser30Cys	missense_variant	2/5		XP_011543138.1
DDIAS	XM_024448400.2	c.89C>G	p.Ser30Cys	missense_variant	3/6		XP_024304168.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDIAS	ENST00000533655.6	c.89C>G	p.Ser30Cys	missense_variant	3/6	1	NM_145018.4	ENSP00000435421.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000277 AC: 4 AN: 1442678 Hom.: 0 Cov.: 29 AF XY: 0.00000139 AC XY: 1 AN XY: 718750

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: 0.00000365

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 18, 2022

The c.89C>G (p.S30C) alteration is located in exon 3 (coding exon 1) of the DDIAS gene. This alteration results from a C to G substitution at nucleotide position 89, causing the serine (S) at amino acid position 30 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.28
BayesDel_addAF	Benign	-0.028	T
BayesDel_noAF	Benign	-0.28
CADD	Uncertain	23
DANN	Benign	0.97
DEOGEN2	Benign	0.19	.;T;.;.;T;.;.;T;.;T
Eigen	Uncertain	0.40
Eigen_PC	Uncertain	0.35
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.89	D;.;D;D;.;D;D;D;D;T
M_CAP	Benign	0.040	D
MetaRNN	Benign	0.39	T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.91	T
PROVEAN	Uncertain	-3.7	D;D;D;D;D;D;D;D;D;.
REVEL	Benign	0.20
Sift	Uncertain	0.0020	D;T;D;T;D;T;T;T;T;.
Sift4G	Benign	0.22	T;T;D;T;D;D;T;T;T;D
Polyphen		1.0, 0.96	.;.;.;D;D;.;.;.;.;D
Vest4		0.69, 0.79, 0.68, 0.83, 0.83
MutPred		0.47		Loss of MoRF binding (P = 0.0858);Loss of MoRF binding (P = 0.0858);Loss of MoRF binding (P = 0.0858);Loss of MoRF binding (P = 0.0858);Loss of MoRF binding (P = 0.0858);.;Loss of MoRF binding (P = 0.0858);Loss of MoRF binding (P = 0.0858);Loss of MoRF binding (P = 0.0858);Loss of MoRF binding (P = 0.0858);
MVP		0.41
MPC		0.25
ClinPred		0.97	D
GERP RS		4.8
Varity_R		0.28
gMVP		0.41

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		Details are displayed if max score is > 0.2

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: chr11-82625869; COSMIC: COSV61272156;