Is LMF1 p.Pro30= (c.90G>T) pathogenic?

LMF1 p.Pro30= (c.90G>T) is classified Likely benign in LMF1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-05-07). Very rare (popmax 0.00292%, nfe); Associated with Cardiovascular phenotype.

What condition is associated with LMF1 p.Pro30= (c.90G>T)?

LMF1 p.Pro30= (c.90G>T) is associated with Cardiovascular phenotype (ClinVar).

How common is LMF1 p.Pro30= (c.90G>T) in the general population?

LMF1 p.Pro30= (c.90G>T) is very rare (popmax 0.00292%, nfe) (gnomAD).

LMF1 p.Pro30=

c.90G>T · rs1264682458 · VCV1765814

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00292%, nfe)

Conditions

Cardiovascular phenotype

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 -2	GERP -1.8
Overall
CADD	2.321	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00292% European (non-Finnish) · 34/1,162,768 alleles

Filtering AF 0.00211% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00186%

Overall 0.00216% 34/1,574,966 alleles · very rare exomes 33/1,422,806 · genomes 1/152,160 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: LMF1
Protein: p.Pro30=
Coding: c.90G>T
MANE Select: NM_022773
dbSNP: rs1264682458
Type: single nucleotide variant
Location: chr16:970891 (GRCh38)
Gene constraint: LOEUF 1.436 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.49
Residue 30: the 'disordered' region

Full LMF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

LMF1 p.Pro30Arg Uncertain significance ★ ⚠ same residue
LMF1 p.Pro30Leu Uncertain significance ★ ⚠ same residue
LMF1 p.Pro30Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
LMF1 p.Arg233Ter Pathogenic/Likely pathogenic ★★ same condition
LMF1 p.Gln299Ter Pathogenic/Likely pathogenic ★★ same condition
LMF1 p.Ala252Val Uncertain significance ★★ same condition
LMF1 p.Ala429Val Uncertain significance ★★ ⚠ same condition
LMF1 p.Ala469Val Uncertain significance ★★ ⚠ 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/lmf1-p-pro30 (accessed [today's date]).

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