rs200434935

Variant names:

• chr2-101697716-ACT-A
• rs200434935
• NM_001395002.1:c.-363_-362delTC

Your query was ambiguous. Multiple possible variants found:

• chr2-101697716-ACT-A
• chr2-101697716-ACT-ACTCT

Variant summary

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

The NM_001395002.1(MAP4K4):​c.-363_-362delTC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 0)
• Consequence: MAP4K4 NM_001395002.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529
• Publications: 0 publications found

Genes affected

MAP4K4 (HGNC:6866): (mitogen-activated protein kinase kinase kinase kinase 4) The protein encoded by this gene is a member of the serine/threonine protein kinase family. This kinase has been shown to specifically activate MAPK8/JNK. The activation of MAPK8 by this kinase is found to be inhibited by the dominant-negative mutants of MAP3K7/TAK1, MAP2K4/MKK4, and MAP2K7/MKK7, which suggests that this kinase may function through the MAP3K7-MAP2K4-MAP2K7 kinase cascade, and mediate the TNF-alpha signaling pathway. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

MAP4K4 Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AD Classification: MODERATE Submitted by: G2P

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395002.1. 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
	MAP4K4	NM_001395002.1	MANE Select	c.-363_-362delTC		5_prime_UTR	Exon 1 of 33	NP_001381931.1	G5E948
	MAP4K4	NM_001384497.1		c.-363_-362delTC		5_prime_UTR	Exon 1 of 32	NP_001371426.1
	MAP4K4	NM_001384492.1		c.-363_-362delTC		5_prime_UTR	Exon 1 of 33	NP_001371421.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP4K4	ENST00000324219.9	TSL:5 MANE Select	c.-363_-362delTC		5_prime_UTR	Exon 1 of 33	ENSP00000313644.6	G5E948
	MAP4K4	ENST00000902131.1		c.-363_-362delTC		5_prime_UTR	Exon 1 of 31	ENSP00000572190.1
	MAP4K4	ENST00000971084.1		c.-363_-362delTC		5_prime_UTR	Exon 1 of 31	ENSP00000641143.1

Frequencies

GnomAD3 genomes Cov.: 0

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

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs200434935; hg19: chr2-102314178;