chrX-72302129-C-T

Variant names:

• chrX-72302129-C-T
• rs2043294470
• NM_001144887.2:c.176G>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001144887.2(CITED1):​c.176G>A​(p.Gly59Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 24)
  • Exomes 𝑓: 9.3e-7 (0 hom. 1 hem.)
  • Failed GnomAD Quality Control
• Consequence: CITED1 NM_001144887.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.00200

Genes affected

CITED1 (HGNC:1986): (Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 1) This gene encodes a member of the CREB-binding protein/p300-interacting transactivator with Asp/Glu-rich C-terminal domain (CITED) family of proteins. The encoded protein, also known as melanocyte-specific gene 1, may function as a transcriptional coactivator and may play a role in pigmentation of melanocytes. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2009]

ENSG00000285547 (HGNC:):

PIN4 (HGNC:8992): (peptidylprolyl cis/trans isomerase, NIMA-interacting 4) This gene encodes a member of the parvulin subfamily of the peptidyl-prolyl cis/trans isomerase protein family. The encoded protein catalyzes the isomerization of peptidylprolyl bonds, and may play a role in the cell cycle, chromatin remodeling, and/or ribosome biogenesis. The encoded protein may play an additional role in the mitochondria. [provided by RefSeq, Dec 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.20759955).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CITED1	NM_001144887.2	c.176G>A	p.Gly59Glu	missense_variant	Exon 3 of 3	ENST00000651998.1	NP_001138359.1
CITED1	NM_001144885.2	c.254G>A	p.Gly85Glu	missense_variant	Exon 4 of 4		NP_001138357.1
CITED1	NM_001144886.2	c.176G>A	p.Gly59Glu	missense_variant	Exon 3 of 3		NP_001138358.1
CITED1	NM_004143.4	c.176G>A	p.Gly59Glu	missense_variant	Exon 3 of 3		NP_004134.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CITED1	ENST00000651998.1	c.176G>A	p.Gly59Glu	missense_variant	Exon 3 of 3		NM_001144887.2	ENSP00000499148.1
ENSG00000285547	ENST00000648922.1	c.1352G>A	p.Gly451Glu	missense_variant	Exon 12 of 12			ENSP00000497072.1

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 9.28e-7 AC: 1 AN: 1077062 Hom.: 0 Cov.: 35 AF XY: 0.00000285 AC XY: 1 AN XY: 350692

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: 0.00000120

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 24

Bravo AF: 0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Oct 12, 2021

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.254G>A (p.G85E) alteration is located in exon 4 (coding exon 3) of the CITED1 gene. This alteration results from a G to A substitution at nucleotide position 254, causing the glycine (G) at amino acid position 85 to be replaced by a glutamic acid (E). 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	0.089
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.56
CADD	Benign	14
DANN	Benign	0.97
DEOGEN2	Benign	0.25	.;.;T;T;T;T;T;.;.
FATHMM_MKL	Benign	0.013	N
LIST_S2	Benign	0.63	.;T;T;.;.;T;T;T;T
M_CAP	Benign	0.015	T
MetaRNN	Benign	0.21	T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.94	T
MutationAssessor	Benign	0.69	.;.;N;N;N;.;.;.;.
PrimateAI	Benign	0.39	T
PROVEAN	Benign	-1.6	N;N;N;N;N;D;D;D;.
REVEL	Benign	0.095
Sift	Benign	0.12	T;T;T;T;T;T;T;T;.
Sift4G	Uncertain	0.015	D;D;D;D;D;.;.;.;.
Polyphen		0.0020	B;B;B;B;B;.;.;.;.
Vest4		0.071
MutPred		0.73		.;.;Gain of solvent accessibility (P = 0.0456);Gain of solvent accessibility (P = 0.0456);Gain of solvent accessibility (P = 0.0456);Gain of solvent accessibility (P = 0.0456);.;.;.;
MVP		0.94
MPC		0.25
ClinPred		0.12	T
GERP RS		2.0
Varity_R		0.13
gMVP		0.32

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2043294470; hg19: chrX-71521979;