Is LPIN2 p.Phe771= (c.2313C>T) pathogenic?

LPIN2 p.Phe771= (c.2313C>T) is classified Likely benign in LPIN2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-23). Absent from gnomAD v4.1; Associated with Majeed syndrome.

What condition is associated with LPIN2 p.Phe771= (c.2313C>T)?

LPIN2 p.Phe771= (c.2313C>T) is associated with Majeed syndrome (ClinVar).

How common is LPIN2 p.Phe771= (c.2313C>T) in the general population?

LPIN2 p.Phe771= (c.2313C>T) is absent from gnomAD v4.1 (gnomAD).

How is Majeed syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

LPIN2 p.Phe771=

c.2313C>T · rs2510241652 · VCV1948917

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Majeed syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.8	GERP 1.9, phastCons 1
Overall
CADD	10.46	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: LPIN2
Protein: p.Phe771=
Coding: c.2313C>T
MANE Select: NM_001375808
dbSNP: rs2510241652
Type: single nucleotide variant
Location: chr18:2922061 (GRCh38)
Gene constraint: LOEUF 0.582 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 61.12
Residue 771: the lns2 domain; the 'c-lip' region

Full LPIN2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Majeed syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Majeed syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy

Similar variants

LPIN2 c.1269-2A>G Likely pathogenic ★★ same condition
LPIN2 c.698+1G>A Likely pathogenic ★★ same condition
LPIN2 c.699-2A>G Likely pathogenic ★★ same condition
LPIN2 p.Arg157Ter Pathogenic ★★ same condition
LPIN2 p.Arg197Ter Pathogenic/Likely pathogenic ★★ same condition
LPIN2 p.Arg280Ter Pathogenic/Likely pathogenic ★★ same condition
LPIN2 p.Arg517His Pathogenic/Likely pathogenic ★★ ⚠ same condition
LPIN2 p.Ser734Leu Pathogenic/Likely pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/lpin2-p-phe771 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown