PABIR2 p.Ala212Val

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is . The variant received -5 ACMG points: 0P and 5B. BP4BS2

The NM_001387468.1(PABIR2):c.635C>T(p.Ala212Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000953 in 1,196,219 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 32 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A212T) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.00012 ( 0 hom., 2 hem., cov: 23)

Exomes 𝑓: 0.000093 ( 0 hom. 30 hem. )

Consequence

PABIR2
NM_001387468.1 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.25

Publications

7 publications found

Variant links:

Genes affected

PABIR2 (HGNC:30490): (PABIR family member 2) Predicted to enable protein serine/threonine phosphatase inhibitor activity. Predicted to be involved in negative regulation of catalytic activity. Predicted to be part of collagen trimer. [provided by Alliance of Genome Resources, Apr 2022]

PABIR2 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_001387468.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -5 ACMG points.

BP4

Computational evidence support a benign effect (REVEL=0.212).

BS2

High Hemizygotes in GnomAd4 at 2 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001387468.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PABIR2	NM_001387468.1	MANE Select	c.635C>T	p.Ala212Val	missense	Exon 9 of 10	NP_001374397.1	G1UD79
PABIR2	NM_001331088.1		c.647C>T	p.Ala216Val	missense	Exon 9 of 10	NP_001318017.1
PABIR2	NM_001331089.1		c.644C>T	p.Ala215Val	missense	Exon 9 of 10	NP_001318018.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PABIR2	ENST00000343004.10	TSL:1 MANE Select	c.635C>T	p.Ala212Val	missense	Exon 9 of 10	ENSP00000339207.6	G1UD79
PABIR2	ENST00000370790.5	TSL:1	c.575C>T	p.Ala192Val	missense	Exon 8 of 9	ENSP00000359826.1	Q7Z309-1
PABIR2	ENST00000896544.1		c.644C>T	p.Ala215Val	missense	Exon 9 of 10	ENSP00000566603.1

Frequencies

GnomAD3 genomes

AF:

0.000117

AC:

AN:

110911

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000164

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000764

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000755

Gnomad OTH

AF:

0.00134

GnomAD2 exomes

AF:

0.000141

AC:

AN:

177686

AF XY:

0.000112

show subpopulations

Gnomad AFR exome

AF:

0.000232

Gnomad AMR exome

AF:

0.000152

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000249

Gnomad OTH exome

AF:

0.00114

GnomAD4 exome

AF:

0.0000931

AC:

101

AN:

1085256

Hom.:

Cov.:

AF XY:

0.0000849

AC XY:

AN XY:

353424

show subpopulations

African (AFR)

AF:

0.0000381

AC:

AN:

26217

American (AMR)

AF:

0.000115

AC:

AN:

34736

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19093

East Asian (EAS)

AF:

0.0000333

AC:

AN:

30022

South Asian (SAS)

AF:

0.000577

AC:

AN:

51999

European-Finnish (FIN)

AF:

0.00

AC:

AN:

39508

Middle Eastern (MID)

AF:

0.000491

AC:

AN:

4075

European-Non Finnish (NFE)

AF:

0.0000611

AC:

AN:

834060

Other (OTH)

AF:

0.000263

AC:

AN:

45546

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.428

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000117

AC:

AN:

110963

Hom.:

Cov.:

AF XY:

0.0000602

AC XY:

AN XY:

33249

show subpopulations

African (AFR)

AF:

0.000163

AC:

AN:

30589

American (AMR)

AF:

0.00

AC:

AN:

10334

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2639

East Asian (EAS)

AF:

0.00

AC:

AN:

3583

South Asian (SAS)

AF:

0.000766

AC:

AN:

2611

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5840

Middle Eastern (MID)

AF:

0.00

AC:

AN:

217

European-Non Finnish (NFE)

AF:

0.0000755

AC:

AN:

52961

Other (OTH)

AF:

0.00133

AC:

AN:

1506

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0000434

Hom.:

Bravo

AF:

0.000102

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.087

BayesDel_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.66

CADD

Benign

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.13

FATHMM_MKL

Uncertain

0.92

LIST_S2

Benign

0.83

M_CAP

Pathogenic

0.40

MetaRNN

Benign

0.12

MetaSVM

Benign

-0.96

MutationAssessor

Uncertain

2.4

PhyloP100

6.3

PrimateAI

Benign

0.32

PROVEAN

Benign

-0.73

REVEL

Benign

0.21

Sift

Benign

0.079

Sift4G

Uncertain

0.037

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Varity_R

0.092

gMVP

0.26

Mutation Taster

=98/2

polymorphism

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over