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NM_001366722.1(GRIP1):c.160G>A (p.Val54Ile) AND Abnormal brain morphology

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Jan 6, 2020
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV000454212.3

Allele description [Variation Report for NM_001366722.1(GRIP1):c.160G>A (p.Val54Ile)]

NM_001366722.1(GRIP1):c.160G>A (p.Val54Ile)

Gene:
GRIP1:glutamate receptor interacting protein 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q14.3
Genomic location:
Preferred name:
NM_001366722.1(GRIP1):c.160G>A (p.Val54Ile)
HGVS:
  • NC_000012.12:g.66541927C>T
  • NG_021400.2:g.532339G>A
  • NM_001178074.2:c.160G>A
  • NM_001366722.1:c.160G>AMANE SELECT
  • NM_001366723.1:c.238G>A
  • NM_001366724.1:c.238G>A
  • NM_021150.4:c.160G>A
  • NP_001171545.1:p.Val54Ile
  • NP_001353651.1:p.Val54Ile
  • NP_001353652.1:p.Val80Ile
  • NP_001353653.1:p.Val80Ile
  • NP_066973.2:p.Val54Ile
  • NC_000012.11:g.66935707C>T
  • NG_021400.1:g.142219G>A
  • NM_001178074.1:c.160G>A
  • NM_021150.3:c.160G>A
Protein change:
V54I
Links:
dbSNP: rs199768740
NCBI 1000 Genomes Browser:
rs199768740
Molecular consequence:
  • NM_001178074.2:c.160G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001366722.1:c.160G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001366723.1:c.238G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001366724.1:c.238G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_021150.4:c.160G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Abnormal brain morphology
Synonyms:
Abnormality of brain morphology
Identifiers:
MedGen: C4021085; Human Phenotype Ontology: HP:0012443

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001142434Reproductive Health Research and Development, BGI Genomics
no assertion criteria provided
Uncertain significance
(Jan 6, 2020) 		germlinecuration

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration
not providedinheritedyesnot providednot providednot providednot providednot providedresearch

Citations

PubMed

Genes that Affect Brain Structure and Function Identified by Rare Variant Analyses of Mendelian Neurologic Disease.

Karaca E, Harel T, Pehlivan D, Jhangiani SN, Gambin T, Coban Akdemir Z, Gonzaga-Jauregui C, Erdin S, Bayram Y, Campbell IM, Hunter JV, Atik MM, Van Esch H, Yuan B, Wiszniewski W, Isikay S, Yesil G, Yuregir OO, Tug Bozdogan S, Aslan H, Aydin H, Tos T, et al.

Neuron. 2015 Nov 4;88(3):499-513. doi: 10.1016/j.neuron.2015.09.048.

PubMed [citation]
PMID:
26539891
PMCID:
PMC4824012

Details of each submission

From Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine, SCV000537996.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyesnot providedBloodnot providednot providednot providednot providednot provided

From Reproductive Health Research and Development, BGI Genomics, SCV001142434.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

NM_021150.3:c.160G>A in the GRIP1 gene has an allele frequency of 0.006 in Ashkenazi Jewish subpopulation in the gnomAD database. Karaca et al. identified c.160G>A compound with c.1142G>T (phase unknown) in a neurologic patient. Two variants are novel with high frequency in Turkish Exomes (PMID: 26539891). We interpret it as a variant of uncertain significance. ACMG/AMP criteria applied: Null.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Flagged submissions

Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000537996Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine
flagged submission
Reason: Outlier claim with insufficient supporting evidence
Notes: None

(Karaca et al. (Neuron 2015))		Likely pathogenicinheritedresearch

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

Last Updated: Feb 28, 2024