X-84321977-A-T

Position:

• chrX-84321977-A-T

Variant summary

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

The NM_001177479.2(HDX):​c.1985T>A​(p.Met662Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000000938 in 1,066,664 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 22)
  • Exomes 𝑓: 9.4e-7 (0 hom. 0 hem.)
• Consequence: HDX NM_001177479.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.21

Genes affected

HDX (HGNC:26411): (highly divergent homeobox) Predicted to enable DNA-binding transcription factor 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. Predicted to be located in nucleus. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]

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/exons	MANE	Protein	UniProt
HDX	NM_001177479.2	c.1985T>A	p.Met662Lys	missense_variant	11/11	ENST00000373177.3	NP_001170950.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HDX	ENST00000373177.3	c.1985T>A	p.Met662Lys	missense_variant	11/11	1	NM_001177479.2	ENSP00000362272	P1
HDX	ENST00000297977.9	c.1985T>A	p.Met662Lys	missense_variant	10/10	1		ENSP00000297977	P1
HDX	ENST00000506585.6	c.1811T>A	p.Met604Lys	missense_variant	10/10	2		ENSP00000423670

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome AF: 9.38e-7 AC: 1 AN: 1066664 Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0 AN XY: 336010

Gnomad4 AFR exome AF: 0.0000391

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 22

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2024

HDX: PM2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
BayesDel_addAF	Benign	-0.016	T
BayesDel_noAF	Benign	-0.26
CADD	Benign	18
DANN	Benign	0.96
DEOGEN2	Uncertain	0.45	T;.;T
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Benign	0.79	.;T;T
M_CAP	Uncertain	0.14	D
MetaRNN	Uncertain	0.47	T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.7	L;.;L
MutationTaster	Benign	1.0	D;D;D
PrimateAI	Uncertain	0.74	T
PROVEAN	Uncertain	-2.4	N;.;.
REVEL	Benign	0.22
Sift	Uncertain	0.0010	D;.;.
Sift4G	Uncertain	0.025	D;D;D
Polyphen		0.44	B;.;B
Vest4		0.57
MutPred		0.29		Gain of ubiquitination at M662 (P = 0.0018);.;Gain of ubiquitination at M662 (P = 0.0018);
MVP		0.39
MPC		0.25
ClinPred		0.92	D
GERP RS		5.5
Varity_R		0.92
gMVP		0.23

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-83576985;