NM_173551.5(ANKS6):c.539_540del (p.Leu180fs) AND Nephronophthisis 16

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 10, 2022
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:: RCV000818335.4

Allele description [Variation Report for NM_173551.5(ANKS6):c.539_540del (p.Leu180fs)]

NM_173551.5(ANKS6):c.539_540del (p.Leu180fs)

Gene:

ANKS6:ankyrin repeat and sterile alpha motif domain containing 6 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

9q22.33

Genomic location:

Preferred name:

NM_173551.5(ANKS6):c.539_540del (p.Leu180fs)

HGVS:

NC_000009.12:g.98790426_98790427del
NG_042237.1:g.11116_11117del
NM_173551.5:c.539_540delMANE SELECT
NP_775822.3:p.Leu180fs
NC_000009.11:g.101552708_101552709del
NM_173551.4:c.539_540del

Protein change:

L180fs

Links:

dbSNP: rs1588420907

NCBI 1000 Genomes Browser:

rs1588420907

Molecular consequence:

NM_173551.5:c.539_540del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Nephronophthisis 16 (NPHP16)
Identifiers:: MONDO: MONDO:0014158; MedGen: C3809320; Orphanet: 655; OMIM: 615382

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000958942	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 10, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 23793029, 25599650, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000958942

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 10, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Citations

PubMed

ANKS6 is a central component of a nephronophthisis module linking NEK8 to INVS and NPHP3.

Hoff S, Halbritter J, Epting D, Frank V, Nguyen TM, van Reeuwijk J, Boehlke C, Schell C, Yasunaga T, Helmstädter M, Mergen M, Filhol E, Boldt K, Horn N, Ueffing M, Otto EA, Eisenberger T, Elting MW, van Wijk JA, Bockenhauer D, Sebire NJ, Rittig S, et al.

Nat Genet. 2013 Aug;45(8):951-6. doi: 10.1038/ng.2681. Epub 2013 Jun 23.

PubMed [citation]

PMID:: 23793029
PMCID:: PMC3786259

ANKS6 is the critical activator of NEK8 kinase in embryonic situs determination and organ patterning.

Czarnecki PG, Gabriel GC, Manning DK, Sergeev M, Lemke K, Klena NT, Liu X, Chen Y, Li Y, San Agustin JT, Garnaas MK, Francis RJ, Tobita K, Goessling W, Pazour GJ, Lo CW, Beier DR, Shah JV.

Nat Commun. 2015 Jan 20;6:6023. doi: 10.1038/ncomms7023.

PubMed [citation]

PMID:: 25599650
PMCID:: PMC4361001

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV000958942.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 661012). This variant has not been reported in the literature in individuals affected with ANKS6-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Leu180Argfs*8) in the ANKS6 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ANKS6 are known to be pathogenic (PMID: 23793029, 25599650).

#	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: Feb 20, 2024

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