chr22-36292059-T-G

Variant names:

• chr22-36292059-T-G
• rs867593888
• NM_002473.6:c.4271A>C

Variant summary

Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Moderate

The NM_002473.6(MYH9):​c.4271A>C​(p.Asp1424Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D1424E) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 33)
• Consequence: MYH9 NM_002473.6 missense
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 8.01
• Publications: 0 publications found

Genes affected

MYH9 (HGNC:7579): (myosin heavy chain 9) This gene encodes a conventional non-muscle myosin; this protein should not be confused with the unconventional myosin-9a or 9b (MYO9A or MYO9B). The encoded protein is a myosin IIA heavy chain that contains an IQ domain and a myosin head-like domain which is involved in several important functions, including cytokinesis, cell motility and maintenance of cell shape. Defects in this gene have been associated with non-syndromic sensorineural deafness autosomal dominant type 17, Epstein syndrome, Alport syndrome with macrothrombocytopenia, Sebastian syndrome, Fechtner syndrome and macrothrombocytopenia with progressive sensorineural deafness. [provided by RefSeq, Dec 2011]

MYH9 Gene-Disease associations (from GenCC):

• autosomal dominant nonsyndromic hearing loss 17

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae), ClinGen
• May-Hegglin anomaly

  Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
• autosomal dominant nonsyndromic hearing loss

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 12 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 5 uncertain in NM_002473.6
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr22-36292058-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 1684413.Status of the report is no_assertion_criteria_provided, 0 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.974
• PP5: Variant 22-36292059-T-G is Pathogenic according to our data. Variant chr22-36292059-T-G is described in CliVar as Pathogenic. Clinvar id is 3068367.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-36292059-T-G is described in CliVar as Pathogenic. Clinvar id is 3068367.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-36292059-T-G is described in CliVar as Pathogenic. Clinvar id is 3068367.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-36292059-T-G is described in CliVar as Pathogenic. Clinvar id is 3068367.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-36292059-T-G is described in CliVar as Pathogenic. Clinvar id is 3068367.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-36292059-T-G is described in CliVar as Pathogenic. Clinvar id is 3068367.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-36292059-T-G is described in CliVar as Pathogenic. Clinvar id is 3068367.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-36292059-T-G is described in CliVar as Pathogenic. Clinvar id is 3068367.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-36292059-T-G is described in CliVar as Pathogenic. Clinvar id is 3068367.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-36292059-T-G is described in CliVar as Pathogenic. Clinvar id is 3068367.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-36292059-T-G is described in CliVar as Pathogenic. Clinvar id is 3068367.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-36292059-T-G is described in CliVar as Pathogenic. Clinvar id is 3068367.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-36292059-T-G is described in CliVar as Pathogenic. Clinvar id is 3068367.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-36292059-T-G is described in CliVar as Pathogenic. Clinvar id is 3068367.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-36292059-T-G is described in CliVar as Pathogenic. Clinvar id is 3068367.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-36292059-T-G is described in CliVar as Pathogenic. Clinvar id is 3068367.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-36292059-T-G is described in CliVar as Pathogenic. Clinvar id is 3068367.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-36292059-T-G is described in CliVar as Pathogenic. Clinvar id is 3068367.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-36292059-T-G is described in CliVar as Pathogenic. Clinvar id is 3068367.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-36292059-T-G is described in CliVar as Pathogenic. Clinvar id is 3068367.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYH9	NM_002473.6	c.4271A>C	p.Asp1424Ala	missense_variant	Exon 31 of 41	ENST00000216181.11	NP_002464.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYH9	ENST00000216181.11	c.4271A>C	p.Asp1424Ala	missense_variant	Exon 31 of 41	1	NM_002473.6	ENSP00000216181.6
MYH9	ENST00000685801.1	c.4334A>C	p.Asp1445Ala	missense_variant	Exon 32 of 42			ENSP00000510688.1
MYH9	ENST00000691109.1	n.4566A>C		non_coding_transcript_exon_variant	Exon 25 of 35

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss Pathogenic:1

May 24, 2023

MVZ Medizinische Genetik Mainz

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ACMG Criteria: PP3_STR,PM1,PM5,PM2_SUP,PP4 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.93
BayesDel_addAF	Pathogenic	0.30	D
BayesDel_noAF	Pathogenic	0.20
CADD	Pathogenic	29
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.80	D
Eigen	Uncertain	0.54
Eigen_PC	Uncertain	0.50
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.89	D
M_CAP	Pathogenic	0.93	D
MetaRNN	Pathogenic	0.97	D
MetaSVM	Uncertain	0.42	D
MutationAssessor	Pathogenic	4.1	H
PhyloP100		8.0
PrimateAI	Uncertain	0.63	T
PROVEAN	Pathogenic	-7.1	D
REVEL	Pathogenic	0.95
Sift	Uncertain	0.017	D
Sift4G	Pathogenic	0.0010	D
Polyphen		1.0	D
Vest4		0.88
MutPred		0.80		Loss of loop (P = 0.1258);
MVP		0.89
MPC		1.6
ClinPred		1.0	D
GERP RS		4.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.8
Varity_R		0.77
gMVP		0.67
Mutation Taster		=19/81	disease causing

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: rs867593888; hg19: chr22-36688105;