NM_001077365.2(POMT1):c.697_699del (p.Asn233del) AND not provided

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: May 12, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV003441850.5

Allele description [Variation Report for NM_001077365.2(POMT1):c.697_699del (p.Asn233del)]

NM_001077365.2(POMT1):c.697_699del (p.Asn233del)

Gene:

POMT1:protein O-mannosyltransferase 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

9q34.13

Genomic location:

Preferred name:

NM_001077365.2(POMT1):c.697_699del (p.Asn233del)

HGVS:

NC_000009.12:g.131509994_131509996del
NG_008896.1:g.12093_12095del
NM_001077365.2:c.697_699delMANE SELECT
NM_001077366.2:c.535_537del
NM_001136113.2:c.697_699del
NM_001136114.2:c.346_348del
NM_001353193.2:c.697_699del
NM_001353194.2:c.535_537del
NM_001353195.2:c.346_348del
NM_001353196.2:c.607_609del
NM_001353197.2:c.535_537del
NM_001353198.2:c.535_537del
NM_001353199.2:c.346_348del
NM_001353200.2:c.241_243del
NM_001374689.1:c.535_537del
NM_001374690.1:c.697_699del
NM_001374691.1:c.346_348del
NM_001374692.1:c.346_348del
NM_001374693.1:c.535_537del
NM_001374695.1:c.241_243del
NM_007171.4:c.697_699del
NP_001070833.1:p.Asn233del
NP_001070834.1:p.Asn179del
NP_001129585.1:p.Asn233del
NP_001129586.1:p.Asn116del
NP_001129586.1:p.Asn116del
NP_001340122.2:p.Asn233del
NP_001340123.1:p.Asn179del
NP_001340124.1:p.Asn116del
NP_001340125.1:p.Asn203del
NP_001340126.2:p.Asn179del
NP_001340127.2:p.Asn179del
NP_001340128.2:p.Asn116del
NP_001340129.1:p.Asn81del
NP_001361618.1:p.Asn179del
NP_001361619.1:p.Asn233del
NP_001361620.1:p.Asn116del
NP_001361621.1:p.Asn116del
NP_001361622.1:p.Asn179del
NP_001361624.1:p.Asn81del
NP_009102.4:p.Asn233del
LRG_842t1:c.697_699del
LRG_842t2:c.697_699del
LRG_842p1:p.Asn233del
LRG_842p2:p.Asn233del
NC_000009.11:g.134385381_134385383del
NM_001136114.1:c.346_348del
NM_007171.3:c.697_699del
NM_007171.3:c.697_699delAAT
NR_148391.2:n.731_733del
NR_148392.2:n.883_885del
NR_148393.2:n.731_733del
NR_148394.2:n.619_621del
NR_148395.2:n.883_885del
NR_148396.2:n.512_514del
NR_148397.2:n.776_778del
NR_148398.2:n.731_733del
NR_148399.2:n.1123_1125del
NR_148400.2:n.717_719del

Protein change:

N116del

Links:

dbSNP: rs761863400

NCBI 1000 Genomes Browser:

rs761863400

Molecular consequence:

NM_001077365.2:c.697_699del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001077366.2:c.535_537del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001136113.2:c.697_699del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001136114.2:c.346_348del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001353193.2:c.697_699del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001353194.2:c.535_537del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001353195.2:c.346_348del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001353196.2:c.607_609del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001353197.2:c.535_537del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001353198.2:c.535_537del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001353199.2:c.346_348del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001353200.2:c.241_243del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001374689.1:c.535_537del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001374690.1:c.697_699del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001374691.1:c.346_348del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001374692.1:c.346_348del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001374693.1:c.535_537del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001374695.1:c.241_243del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_007171.4:c.697_699del - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_148391.2:n.731_733del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148392.2:n.883_885del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148393.2:n.731_733del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148394.2:n.619_621del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148395.2:n.883_885del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148396.2:n.512_514del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148397.2:n.776_778del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148398.2:n.731_733del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148399.2:n.1123_1125del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148400.2:n.717_719del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004170064	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (May 12, 2023)	germline	clinical testing	Citation Link,
SCV004229900	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Uncertain significance (Sep 27, 2022)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 34930662, 26467025
SCV004236458	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Feb 27, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004170064

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(May 12, 2023)

germline

clinical testing

Citation Link,

SCV004229900

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Uncertain significance
(Sep 27, 2022)

unknown

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV004236458

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Feb 27, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Genome sequencing as a first-line diagnostic test for hospitalized infants.

Bowling KM, Thompson ML, Finnila CR, Hiatt SM, Latner DR, Amaral MD, Lawlor JMJ, East KM, Cochran ME, Greve V, Kelley WV, Gray DE, Felker SA, Meddaugh H, Cannon A, Luedecke A, Jackson KE, Hendon LG, Janani HM, Johnston M, Merin LA, Deans SL, et al.

Genet Med. 2022 Apr;24(4):851-861. doi: 10.1016/j.gim.2021.11.020. Epub 2021 Nov 27.

PubMed [citation]

PMID:: 34930662
PMCID:: PMC8995345

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

See all PubMed Citations (3)

Details of each submission

From GeneDx, SCV004170064.1

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

Description

Observed with a pathogenic variant on the opposite allele (in trans) in a hospitalized infant in published literature, although clinical information was not provided (Bowling et al., 2022); In-frame deletion of 1 amino acid in a non-repeat region; Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on protein structure/function; In-silico analysis is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown; This variant is associated with the following publications: (PMID: 34930662)

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

From Athena Diagnostics, SCV004229900.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

Available data are insufficient to determine the clinical significance of the variant at this time. The frequency of this variant in the general population is uninformative in assessment of its pathogenicity (http://gnomad.broadinstitute.org). Computational tools disagree on the variant's effect on normal protein function.

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

From Revvity Omics, Revvity, SCV004236458.1

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

#	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: Jan 13, 2025

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