20-18162473-T-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 1P and 12B. PP2BP4_StrongBA1

The NM_001392073.1(KAT14):c.1196T>G(p.Val399Gly) variant causes a missense change. The variant allele was found at a frequency of 0.98 in 1,614,088 control chromosomes in the GnomAD database, including 774,757 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.98 ( 73697 hom., cov: 31)

Exomes 𝑓: 0.98 ( 701060 hom. )

Consequence

KAT14
NM_001392073.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.05

Publications

30 publications found

Variant links:

Genes affected

KAT14 (HGNC:15904): (lysine acetyltransferase 14) CSRP2 is a protein containing two LIM domains, which are double zinc finger motifs found in proteins of diverse function. CSRP2 and some related proteins are thought to act as protein adapters, bridging two or more proteins to form a larger protein complex. The protein encoded by this gene binds to one of the LIM domains of CSRP2 and contains an acetyltransferase domain. Although the encoded protein has been detected in the cytoplasm, it is predominantly a nuclear protein. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jun 2011]

KAT14 Gene-Disease associations (from GenCC):

multiple congenital anomalies/dysmorphic syndrome
Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

KAT14 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

PP2

Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 1 curated pathogenic missense variants (we use a threshold of 10). The gene has 0 curated benign missense variants. Gene score misZ: 0.77498 (below the threshold of 3.09). Trascript score misZ: 1.7338 (below the threshold of 3.09). GenCC associations: The gene is linked to multiple congenital anomalies/dysmorphic syndrome.

BP4

Computational evidence support a benign effect (MetaRNN=5.7861917E-7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.987 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001392073.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
KAT14	NM_001392073.1	MANE Select	c.1196T>G	p.Val399Gly	missense	Exon 7 of 11	NP_001379002.1	A0A075B6H4
KAT14	NM_001384192.3		c.1199T>G	p.Val400Gly	missense	Exon 7 of 11	NP_001371121.2	Q9H8E8-1
KAT14	NM_001392069.1		c.1199T>G	p.Val400Gly	missense	Exon 7 of 11	NP_001378998.1	Q9H8E8-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
KAT14	ENST00000688188.1	MANE Select	c.1196T>G	p.Val399Gly	missense	Exon 7 of 11	ENSP00000508684.1	A0A075B6H4
KAT14	ENST00000435364.8	TSL:1	c.1199T>G	p.Val400Gly	missense	Exon 7 of 11	ENSP00000392318.2	Q9H8E8-1
KAT14	ENST00000489634.2	TSL:1	c.815T>G	p.Val272Gly	missense	Exon 5 of 9	ENSP00000425909.2	Q9H8E8-2

Frequencies

GnomAD3 genomes

AF:

0.984

AC:

149667

AN:

152112

Hom.:

73637

Cov.:

show subpopulations

Gnomad AFR

AF:

0.995

Gnomad AMI

AF:

0.984

Gnomad AMR

AF:

0.977

Gnomad ASJ

AF:

0.974

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.992

Gnomad FIN

AF:

0.986

Gnomad MID

AF:

0.975

Gnomad NFE

AF:

0.977

Gnomad OTH

AF:

0.982

GnomAD2 exomes

AF:

0.984

AC:

247112

AN:

251234

AF XY:

0.983

show subpopulations

Gnomad AFR exome

AF:

0.996

Gnomad AMR exome

AF:

0.988

Gnomad ASJ exome

AF:

0.974

Gnomad EAS exome

AF:

1.00

Gnomad FIN exome

AF:

0.986

Gnomad NFE exome

AF:

0.976

Gnomad OTH exome

AF:

0.981

GnomAD4 exome

AF:

0.979

AC:

1431629

AN:

1461858

Hom.:

701060

Cov.:

102

AF XY:

0.980

AC XY:

712392

AN XY:

727234

show subpopulations

African (AFR)

AF:

0.996

AC:

33335

AN:

33480

American (AMR)

AF:

0.987

AC:

44151

AN:

44716

Ashkenazi Jewish (ASJ)

AF:

0.973

AC:

25426

AN:

26134

East Asian (EAS)

AF:

1.00

AC:

39695

AN:

39696

South Asian (SAS)

AF:

0.993

AC:

85675

AN:

86256

European-Finnish (FIN)

AF:

0.985

AC:

52600

AN:

53416

Middle Eastern (MID)

AF:

0.963

AC:

5554

AN:

5768

European-Non Finnish (NFE)

AF:

0.977

AC:

1085901

AN:

1111998

Other (OTH)

AF:

0.982

AC:

59292

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

2269

4538

6808

9077

11346

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

21662

43324

64986

86648

108310

<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:

0.984

AC:

149786

AN:

152230

Hom.:

73697

Cov.:

AF XY:

0.984

AC XY:

73210

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.995

AC:

41320

AN:

41522

American (AMR)

AF:

0.977

AC:

14942

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.974

AC:

3380

AN:

3472

East Asian (EAS)

AF:

1.00

AC:

5170

AN:

5170

South Asian (SAS)

AF:

0.992

AC:

4782

AN:

4820

European-Finnish (FIN)

AF:

0.986

AC:

10460

AN:

10604

Middle Eastern (MID)

AF:

0.976

AC:

287

AN:

294

European-Non Finnish (NFE)

AF:

0.977

AC:

66473

AN:

68034

Other (OTH)

AF:

0.982

AC:

2075

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

136

271

407

542

678

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

914

1828

2742

3656

4570

<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:

0.979

Hom.:

151145

Bravo

AF:

0.984

TwinsUK

AF:

0.970

AC:

3598

ALSPAC

AF:

0.977

AC:

3767

ESP6500AA

AF:

0.994

AC:

4381

ESP6500EA

AF:

0.974

AC:

8373

ExAC

AF:

0.984

AC:

119407

Asia WGS

AF:

0.997

AC:

3464

AN:

3476

EpiCase

AF:

0.975

EpiControl

AF:

0.973

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.055

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.68

CADD

Benign

(source)

DANN

Benign

0.84

DEOGEN2

Benign

0.027

Eigen

Benign

-0.36

Eigen_PC

Benign

-0.10

FATHMM_MKL

Benign

0.23

LIST_S2

Benign

0.026

MetaRNN

Benign

5.8e-7

MetaSVM

Benign

-0.96

MutationAssessor

Benign

-0.69

PhyloP100

4.1

PrimateAI

Benign

0.38

PROVEAN

Benign

-0.14

REVEL

Benign

0.097

Sift

Benign

0.55

Sift4G

Benign

0.44

Polyphen

0.0

Vest4

0.051

MPC

0.25

ClinPred

0.0049

GERP RS

6.0

Varity_R

0.042

gMVP

0.18

Mutation Taster

=99/1

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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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