rs367819379

Variant names:

• chr14-64468713-C-A
• rs367819379
• NM_004857.3:c.319C>A

Your query was ambiguous. Multiple possible variants found:

• chr14-64468713-C-A
• chr14-64468713-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_004857.3(AKAP5):​c.319C>A​(p.Pro107Thr) 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. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P107S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: AKAP5 NM_004857.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 2 publications found

Genes affected

AKAP5 (HGNC:375): (A-kinase anchoring protein 5) The A-kinase anchor proteins (AKAPs) are a group of structurally diverse proteins, which have the common function of binding to the regulatory subunit of protein kinase A (PKA) and confining the holoenzyme to discrete locations within the cell. This gene encodes a member of the AKAP family. The encoded protein binds to the RII-beta regulatory subunit of PKA, and also to protein kinase C and the phosphatase calcineurin. It is predominantly expressed in cerebral cortex and may anchor the PKA protein at postsynaptic densities (PSD) and be involved in the regulation of postsynaptic events. It is also expressed in T lymphocytes and may function to inhibit interleukin-2 transcription by disrupting calcineurin-dependent dephosphorylation of NFAT. [provided by RefSeq, Jul 2008]

ZBTB25 (HGNC:13112): (zinc finger and BTB domain containing 25) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08262238).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004857.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AKAP5	NM_004857.3	MANE Select	c.319C>A	p.Pro107Thr	missense	Exon 2 of 2	NP_004848.3	P24588
	ZBTB25	NM_001304508.1		c.174-19075G>T		intron	N/A	NP_001291437.1	G3V2K3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AKAP5	ENST00000394718.4	TSL:1 MANE Select	c.319C>A	p.Pro107Thr	missense	Exon 2 of 2	ENSP00000378207.3	P24588
	ZBTB25	ENST00000555220.5	TSL:1	c.174-19075G>T		intron	N/A	ENSP00000450718.1	G3V2K3
	AKAP5	ENST00000320636.5	TSL:6	c.319C>A	p.Pro107Thr	missense	Exon 1 of 1	ENSP00000315615.5	P24588

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.068
BayesDel_addAF	Benign	-0.24	T
BayesDel_noAF	Benign	-0.58
CADD	Benign	0.34
DANN	Benign	0.53
DEOGEN2	Uncertain	0.60	D
Eigen	Benign	-0.89
Eigen_PC	Benign	-0.90
FATHMM_MKL	Benign	0.14	N
LIST_S2	Benign	0.43	T
M_CAP	Benign	0.0039	T
MetaRNN	Benign	0.083	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.8	L
PhyloP100		0.013
PrimateAI	Benign	0.22	T
PROVEAN	Pathogenic	-5.2	D
REVEL	Benign	0.051
Sift	Benign	0.077	T
Sift4G	Benign	0.57	T
Polyphen		0.060	B
Vest4		0.063
MutPred		0.20		Gain of catalytic residue at M105 (P = 0.0067)
MVP		0.29
MPC		0.23
ClinPred		0.14	T
GERP RS		1.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.14
gMVP		0.074
Mutation Taster		=95/5	polymorphism

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

Other links and lift over

dbSNP: rs367819379; hg19: chr14-64935431;