NM_018195.4:c.763A>G

Variant names:

• chr11-112082853-A-G
• NM_018195.4:c.763A>G
• NKAPD1 p.Arg255Gly

GermlineCancer (beta)

Variant summary

Our verdict is Uncertain significance.

0 Uncertain · Cold

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received 0 classification points (ACMG Germline Pathogenicity v2019). PM2BP4_Moderate

The NM_018195.4(NKAPD1):c.763A>G (p.Arg255Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. In-silico predictor (REVEL) classifies this variant as likely benign. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: NKAPD1 NM_018195.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.31
• Publications: 0 publications found

Genes affected

NKAPD1 (HGNC:25569): (NKAP domain containing 1) Enables identical protein binding activity. [provided by Alliance of Genome Resources, Jul 2025]

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 0 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	PM2Absent/extremely low in population databases		Absent from gnomAD (AR/unknown gene) — PM2; Absent from gnomAD at well-covered site (MOI: unknown) (threshold 0.001) — PM2 moderate.
	BP4Computational evidence suggests no impact		Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); Splicing verdict: benign (Strong).; Germline computational verdict: benign (Moderate).

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_018195.4. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	NKAPD1 NM_018195.4	MANE Select	c.763A>G p.Arg255Gly	missense	Exon 6 of 6	Prot: NP_060665.3
	NKAPD1 NM_001082969.2		c.763A>G p.Arg255Gly	missense	Exon 6 of 6	Prot: NP_001076438.1 UniProt:
	NKAPD1 NM_001082970.2		c.760A>G p.Arg254Gly	missense	Exon 6 of 6	Prot: NP_001076439.1 UniProt:

NKAPD1 NM_018195.4

MANE Select

HGVSc / HGVSpc.763A>Gp.Arg255Gly

Exon rankExon 6 of 6

missense

Prot: NP_060665.3

NKAPD1 NM_001082969.2

HGVSc / HGVSpc.763A>Gp.Arg255Gly

Exon rankExon 6 of 6

missense

Prot: NP_001076438.1UniProt: Q6ZUT1-2

NKAPD1 NM_001082970.2

HGVSc / HGVSpc.760A>Gp.Arg254Gly

Exon rankExon 6 of 6

missense

Prot: NP_001076439.1UniProt: Q6ZUT1-1

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	NKAPD1 ENST00000393047.8	TSL:1MANE Select	c.763A>G p.Arg255Gly	missense	Exon 6 of 6	Prot: ENSP00000376767.3 UniProt:
	NKAPD1 ENST00000420986.6	TSL:1	c.760A>G p.Arg254Gly	missense	Exon 6 of 6	Prot: ENSP00000402208.2 UniProt:
	NKAPD1 ENST00000968797.1		c.790A>G p.Arg264Gly	missense	Exon 6 of 6	Prot: ENSP00000638856.1 UniProt:

NKAPD1 ENST00000393047.8

TSL:1MANE Select

HGVSc / HGVSpc.763A>Gp.Arg255Gly

Exon rankExon 6 of 6

missense

Prot: ENSP00000376767.3UniProt: Q6ZUT1-2

NKAPD1 ENST00000420986.6

TSL:1

HGVSc / HGVSpc.760A>Gp.Arg254Gly

Exon rankExon 6 of 6

missense

Prot: ENSP00000402208.2UniProt: Q6ZUT1-1

NKAPD1 ENST00000968797.1

HGVSc / HGVSpc.790A>Gp.Arg264Gly

Exon rankExon 6 of 6

missense

Prot: ENSP00000638856.1UniProt: A0ACI8VP42

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 3 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:32
GnomAD4 exome	AF:	AC:	Hom:	AN:	Cov:31
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:32

Showing 3 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Uncertain	17
AlphaMissense	Benign	0.090
BayesDel_addAF	Benign	-0.17	T
BayesDel_noAF	Benign	-0.48
CADD	Benign	22
DANN	Uncertain	0.99
DEOGEN2	Benign	0.065	T
Eigen	Benign	-0.30
Eigen_PC	Benign	-0.13
FATHMM_MKL	Uncertain	0.89	D
FuncVEP CTI	Benign	0.0087
GPN-Star LLR	N/A	-4.2
GPN-Star score	N/A	4.2
LIST_S2	Benign	0.75	T
M_CAP	Benign	0.0015	T
MetaRNN	Benign	0.084	T
MetaSVM	Benign	-1.1	T
Mutation Taster	N/A	80/20	polymorphism
PhyloP100	Benign	2.3
popEVE	Benign	-3.4
PROVEAN	Benign	-1.7	N
REVEL	Benign	0.054
Sift	Uncertain	0.0080	D
Sift4G	Uncertain	0.042	D
Varity_R	N/A	0.089
VESM-3B	Benign	-4.9

Showing 26 of 26 scores

Splicing Scores

Algorithm	Calibrated pred.	Score	Prediction
Pangolin (max)	Benign	0.0
SpliceAI score (max)	Benign	0.0	Details are displayed if max score is > 0.2

Showing 2 of 2 scores

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.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

hg19: chr11-111953577;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar