NM_001395002.1(MAP4K4):c.2638G>A (p.Ala880Thr) AND Inborn genetic diseases

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 15, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003376972.2

Allele description [Variation Report for NM_001395002.1(MAP4K4):c.2638G>A (p.Ala880Thr)]

NM_001395002.1(MAP4K4):c.2638G>A (p.Ala880Thr)

Genes:

LOC122817718:Sharpr-MPRA regulatory region 3767 [Gene]
MAP4K4:mitogen-activated protein kinase kinase kinase kinase 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q11.2

Genomic location:

Preferred name:

NM_001395002.1(MAP4K4):c.2638G>A (p.Ala880Thr)

HGVS:

NC_000002.12:g.101869796G>A
NG_076990.1:g.270G>A
NM_001242559.2:c.2395G>A
NM_001242560.2:c.2383G>A
NM_001384476.1:c.2473G>A
NM_001384477.1:c.2470G>A
NM_001384478.1:c.2152G>A
NM_001384480.1:c.2152G>A
NM_001384481.1:c.2398G>A
NM_001384482.1:c.2143G>A
NM_001384483.1:c.2233G>A
NM_001384484.1:c.2476G>A
NM_001384485.1:c.2476G>A
NM_001384486.1:c.2407G>A
NM_001384487.1:c.2374G>A
NM_001384488.1:c.2404G>A
NM_001384489.1:c.1654G>A
NM_001384490.1:c.2245G>A
NM_001384491.1:c.2380G>A
NM_001384492.1:c.2542G>A
NM_001384493.1:c.2476G>A
NM_001384494.1:c.2242G>A
NM_001384495.1:c.2152G>A
NM_001384496.1:c.2236G>A
NM_001384497.1:c.2629G>A
NM_001384505.1:c.1114G>A
NM_001384506.1:c.2638G>A
NM_001384507.1:c.2407G>A
NM_001384508.1:c.2470G>A
NM_001384509.1:c.2371G>A
NM_001384520.1:c.2536G>A
NM_001384543.1:c.2545G>A
NM_001384544.1:c.1561G>A
NM_001384545.1:c.1561G>A
NM_001384548.1:c.2389G>A
NM_001384549.1:c.2125G>A
NM_001384550.1:c.2362G>A
NM_001384551.1:c.2287G>A
NM_001384552.1:c.2446G>A
NM_001384553.1:c.2443G>A
NM_001384554.1:c.2347G>A
NM_001384555.1:c.2449G>A
NM_001384556.1:c.2440G>A
NM_001384557.1:c.2278G>A
NM_001384558.1:c.2356G>A
NM_001384559.1:c.2122G>A
NM_001384560.1:c.2209G>A
NM_001384561.1:c.2125G>A
NM_001384562.1:c.2443G>A
NM_001384563.1:c.2440G>A
NM_001384564.1:c.2509G>A
NM_001384567.1:c.2356G>A
NM_001384572.1:c.2449G>A
NM_001384579.1:c.2380G>A
NM_001395002.1:c.2638G>AMANE SELECT
NM_004834.5:c.2149G>A
NM_145686.4:c.2305G>A
NM_145687.4:c.2314G>A
NP_001229488.1:p.Ala799Thr
NP_001229489.1:p.Ala795Thr
NP_001371405.1:p.Ala825Thr
NP_001371406.1:p.Ala824Thr
NP_001371407.1:p.Ala718Thr
NP_001371409.1:p.Ala718Thr
NP_001371410.1:p.Ala800Thr
NP_001371411.1:p.Ala715Thr
NP_001371412.1:p.Ala745Thr
NP_001371413.1:p.Ala826Thr
NP_001371414.1:p.Ala826Thr
NP_001371415.1:p.Ala803Thr
NP_001371416.1:p.Ala792Thr
NP_001371417.1:p.Ala802Thr
NP_001371418.1:p.Ala552Thr
NP_001371419.1:p.Ala749Thr
NP_001371420.1:p.Ala794Thr
NP_001371421.1:p.Ala848Thr
NP_001371422.1:p.Ala826Thr
NP_001371423.1:p.Ala748Thr
NP_001371424.1:p.Ala718Thr
NP_001371425.1:p.Ala746Thr
NP_001371426.1:p.Ala877Thr
NP_001371434.1:p.Ala372Thr
NP_001371435.1:p.Ala880Thr
NP_001371436.1:p.Ala803Thr
NP_001371437.1:p.Ala824Thr
NP_001371438.1:p.Ala791Thr
NP_001371449.1:p.Ala846Thr
NP_001371472.1:p.Ala849Thr
NP_001371473.1:p.Ala521Thr
NP_001371474.1:p.Ala521Thr
NP_001371477.1:p.Ala797Thr
NP_001371478.1:p.Ala709Thr
NP_001371479.1:p.Ala788Thr
NP_001371480.1:p.Ala763Thr
NP_001371481.1:p.Ala816Thr
NP_001371482.1:p.Ala815Thr
NP_001371483.1:p.Ala783Thr
NP_001371484.1:p.Ala817Thr
NP_001371485.1:p.Ala814Thr
NP_001371486.1:p.Ala760Thr
NP_001371487.1:p.Ala786Thr
NP_001371488.1:p.Ala708Thr
NP_001371489.1:p.Ala737Thr
NP_001371490.1:p.Ala709Thr
NP_001371491.1:p.Ala815Thr
NP_001371492.1:p.Ala814Thr
NP_001371493.1:p.Ala837Thr
NP_001371496.1:p.Ala786Thr
NP_001371501.1:p.Ala817Thr
NP_001371508.1:p.Ala794Thr
NP_001381931.1:p.Ala880Thr
NP_004825.3:p.Ala717Thr
NP_663719.2:p.Ala769Thr
NP_663720.1:p.Ala772Thr
NC_000002.11:g.102486258G>A
NM_145686.3:c.2305G>A
NR_169279.1:n.2771G>A
NR_169280.1:n.2678G>A
NR_169281.1:n.2678G>A
NR_169282.1:n.2231G>A

Protein change:

A372T

Molecular consequence:

NM_001242559.2:c.2395G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001242560.2:c.2383G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384476.1:c.2473G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384477.1:c.2470G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384478.1:c.2152G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384480.1:c.2152G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384481.1:c.2398G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384482.1:c.2143G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384483.1:c.2233G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384484.1:c.2476G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384485.1:c.2476G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384486.1:c.2407G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384487.1:c.2374G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384488.1:c.2404G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384489.1:c.1654G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384490.1:c.2245G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384491.1:c.2380G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384492.1:c.2542G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384493.1:c.2476G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384494.1:c.2242G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384495.1:c.2152G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384496.1:c.2236G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384497.1:c.2629G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384505.1:c.1114G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384506.1:c.2638G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384507.1:c.2407G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384508.1:c.2470G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384509.1:c.2371G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384520.1:c.2536G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384543.1:c.2545G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384544.1:c.1561G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384545.1:c.1561G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384548.1:c.2389G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384549.1:c.2125G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384550.1:c.2362G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384551.1:c.2287G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384552.1:c.2446G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384553.1:c.2443G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384554.1:c.2347G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384555.1:c.2449G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384556.1:c.2440G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384557.1:c.2278G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384558.1:c.2356G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384559.1:c.2122G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384560.1:c.2209G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384561.1:c.2125G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384562.1:c.2443G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384563.1:c.2440G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384564.1:c.2509G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384567.1:c.2356G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384572.1:c.2449G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384579.1:c.2380G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001395002.1:c.2638G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004834.5:c.2149G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_145686.4:c.2305G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_145687.4:c.2314G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_169279.1:n.2771G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_169280.1:n.2678G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_169281.1:n.2678G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_169282.1:n.2231G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

Recent activity

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tetraspanin-31 isoform 3 precursor [Homo sapiens]
tetraspanin-31 isoform 3 precursor [Homo sapiens]
gi|1064788208|ref|NP_001317098.1|

Protein
Homo sapiens fibronectin leucine rich transmembrane protein 2 (FLRT2), transcrip...
Homo sapiens fibronectin leucine rich transmembrane protein 2 (FLRT2), transcript variant 4, mRNA
gi|1890278092|ref|NM_001346145.2|

Nucleotide
peroxisome proliferator-activated receptor gamma coactivator-related protein 1 i...
peroxisome proliferator-activated receptor gamma coactivator-related protein 1 isoform X16 [Homo sapiens]
gi|2462518060|ref|XP_054221290.1|

Protein
Homo sapiens S100 calcium binding protein A16 (S100A16), transcript variant 2, m...
Homo sapiens S100 calcium binding protein A16 (S100A16), transcript variant 2, mRNA
gi|1890270986|ref|NM_001317008.2|

Nucleotide
Rhizobium sp. ICS20406 16S ribosomal RNA gene, partial sequence
Rhizobium sp. ICS20406 16S ribosomal RNA gene, partial sequence
gi|38374018|gb|AY456208.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004095545	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Aug 15, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004095545

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Aug 15, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV004095545.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The c.2305G>A (p.A769T) alteration is located in exon 20 (coding exon 20) of the MAP4K4 gene. This alteration results from a G to A substitution at nucleotide position 2305, causing the alanine (A) at amino acid position 769 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 1, 2024

ClinVar

Relating variation to medicine