rs149925845

Variant names:

• chr16-31359992-C-A
• rs149925845
• NM_000887.5:c.634C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-31359992-C-A
• chr16-31359992-C-G
• chr16-31359992-C-T

Variant summary

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

The NM_000887.5(ITGAX):​c.634C>A​(p.Pro212Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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: 32)
• Consequence: ITGAX NM_000887.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.12

Genes affected

ITGAX (HGNC:6152): (integrin subunit alpha X) This gene encodes the integrin alpha X chain protein. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. This protein combines with the beta 2 chain (ITGB2) to form a leukocyte-specific integrin referred to as inactivated-C3b (iC3b) receptor 4 (CR4). The alpha X beta 2 complex seems to overlap the properties of the alpha M beta 2 integrin in the adherence of neutrophils and monocytes to stimulated endothelium cells, and in the phagocytosis of complement coated particles. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2013]

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
ITGAX	NM_000887.5	c.634C>A	p.Pro212Thr	missense_variant	Exon 7 of 30	ENST00000268296.9	NP_000878.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGAX	ENST00000268296.9	c.634C>A	p.Pro212Thr	missense_variant	Exon 7 of 30	1	NM_000887.5	ENSP00000268296.5
ITGAX	ENST00000562522.2	c.634C>A	p.Pro212Thr	missense_variant	Exon 7 of 31	1		ENSP00000454623.1
ITGAX	ENST00000571644.1	n.56C>A		non_coding_transcript_exon_variant	Exon 1 of 22	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_addAF	Uncertain	0.039	T
BayesDel_noAF	Benign	-0.18
CADD	Benign	21
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.62	D;.
Eigen	Benign	0.00094
Eigen_PC	Benign	-0.20
FATHMM_MKL	Benign	0.40	N
LIST_S2	Benign	0.72	T;T
M_CAP	Benign	0.054	D
MetaRNN	Uncertain	0.73	D;D
MetaSVM	Benign	-0.35	T
MutationAssessor	Pathogenic	3.3	M;.
PrimateAI	Benign	0.32	T
PROVEAN	Pathogenic	-5.5	D;D
REVEL	Uncertain	0.37
Sift	Benign	0.098	T;T
Sift4G	Benign	0.10	T;T
Polyphen		0.99	D;.
Vest4		0.51
MutPred		0.59		Loss of disorder (P = 0.156);Loss of disorder (P = 0.156);
MVP		0.77
MPC		0.81
ClinPred		0.76	D
GERP RS		3.9
Varity_R		0.82
gMVP		0.82

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs149925845; hg19: chr16-31371313;