rs560912060

Variant names:

• chr1-154273375-AGATGAT-A
• rs560912060
• NM_006118.4:c.99_104delTGATGA

Your query was ambiguous. Multiple possible variants found:

• chr1-154273375-AGATGAT-A
• chr1-154273375-AGATGAT-AGAT

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP3

The NM_006118.4(HAX1):​c.99_104delTGATGA​(p.Asp33_Asp34del) variant causes a disruptive inframe deletion change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. D33D) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 31)
• Consequence: HAX1 NM_006118.4 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.38
• Publications: 0 publications found

Genes affected

HAX1 (HGNC:16915): (HCLS1 associated protein X-1) The protein encoded by this gene is known to associate with hematopoietic cell-specific Lyn substrate 1, a substrate of Src family tyrosine kinases. It also interacts with the product of the polycystic kidney disease 2 gene, mutations in which are associated with autosomal-dominant polycystic kidney disease, and with the F-actin-binding protein, cortactin. It was earlier thought that this gene product is mainly localized in the mitochondria, however, recent studies indicate it to be localized in the cell body. Mutations in this gene result in autosomal recessive severe congenital neutropenia, also known as Kostmann disease. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

HAX1 Gene-Disease associations (from GenCC):

• Kostmann syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP3: Nonframeshift variant in repetitive region in NM_006118.4

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006118.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HAX1	NM_006118.4	MANE Select	c.99_104delTGATGA	p.Asp33_Asp34del	disruptive_inframe_deletion	Exon 2 of 7	NP_006109.2
	HAX1	NM_001018837.2		c.54-99_54-94delTGATGA		intron	N/A	NP_001018238.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HAX1	ENST00000328703.12	TSL:1 MANE Select	c.99_104delTGATGA	p.Asp33_Asp34del	disruptive_inframe_deletion	Exon 2 of 7	ENSP00000329002.7
	HAX1	ENST00000457918.6	TSL:1	c.54-99_54-94delTGATGA		intron	N/A	ENSP00000411448.2
	HAX1	ENST00000483970.7	TSL:2	c.99_104delTGATGA	p.Asp33_Asp34del	disruptive_inframe_deletion	Exon 2 of 7	ENSP00000435088.1

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		4.4

Splicing

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

Other links and lift over

dbSNP: rs560912060; hg19: chr1-154245851;