Is FMN2 p.Ala1072= (c.3216G>A) pathogenic?

FMN2 p.Ala1072= (c.3216G>A) is classified Benign in FMN2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-11-26). Common (popmax 21.4%, sas) — too common for a highly-penetrant pathogenic allele; Associated with intellectual disability, autosomal recessive 47.

What condition is associated with FMN2 p.Ala1072= (c.3216G>A)?

FMN2 p.Ala1072= (c.3216G>A) is associated with intellectual disability, autosomal recessive 47 (ClinVar).

FMN2 p.Ala1072=

Q: How common is FMN2 p.Ala1072= (c.3216G>A) in the general population?

FMN2 p.Ala1072= (c.3216G>A) is common (popmax 21.4%, sas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.3216G>A · rs71646895 · VCV1285276

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Common

common (popmax 21.4%, sas) — too common for a highly-penetrant pathogenic allele

Conditions

intellectual disability, autosomal recessive 47

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 -6.3	GERP -1.1
Overall
CADD	6.418	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 21.4% South Asian · 6,312/29,564 alleles

Filtering AF 20.9% ClinGen BA1/BS1 input FAF95, joint · FAF99 20.7%

Overall 19.9% 46,576/234,454 alleles · common exomes 46,317/228,880 · genomes 259/5,574 · joint denominator

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	33.9%	3
South Asiangrpmax	21.4%	5
European (non-Finnish)	20.6%	5
Remaining individualsnot grpmax-eligible	18.6%	5
Middle Eastern	15.6%	6
Ashkenazi Jewishnot grpmax-eligible	14.7%	7
African / African-American	10.9%	9
Admixed American	8.25%	12
East Asian	4.55%	22

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: FMN2
Protein: p.Ala1072=
Coding: c.3216G>A
MANE Select: NM_020066
dbSNP: rs71646895
Type: single nucleotide variant
Location: chr1:240208028 (GRCh38)
Gene constraint: LOEUF 0.51 · pLI 0.51 (gnomAD)
Structure: AlphaFold pLDDT 51.48 · 2 PDB
Residue 1072: the fh1 domain; the 'disordered' region

Full FMN2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

intellectual disability, autosomal recessive 47 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

FMN2 p.Ile183Phe Likely pathogenic ★★ ⚠ same condition
FMN2 p.Asp352Tyr Uncertain significance ★★ ⚠ same condition
FMN2 p.Gln192Leu Uncertain significance ★★ ⚠ same condition
FMN2 p.Gln210Arg Uncertain significance ★★ ⚠ same condition
FMN2 p.Pro1044Leu Uncertain significance ★★ ⚠ same condition
FMN2 p.Pro1187Leu Uncertain significance ★★ ⚠ same condition
FMN2 p.Thr415Ile Uncertain significance ★★ ⚠ same condition
FMN2 p.Ala471= Benign ★★ 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/fmn2-p-ala1072 (accessed [today's date]).

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