Is FLNA p.Thr2016= (c.6048G>A) pathogenic?

FLNA p.Thr2016= (c.6048G>A) is classified Benign/Likely benign in FLNA (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-01-14). Very rare (popmax 0.00436%, amr); Associated with familial thoracic aortic aneurysm and aortic dissection.

What condition is associated with FLNA p.Thr2016= (c.6048G>A)?

FLNA p.Thr2016= (c.6048G>A) is associated with familial thoracic aortic aneurysm and aortic dissection, heterotopia, periventricular, X-linked dominant, otopalatodigital syndrome type 2 (ClinVar).

How common is FLNA p.Thr2016= (c.6048G>A) in the general population?

FLNA p.Thr2016= (c.6048G>A) is very rare (popmax 0.00436%, amr) (gnomAD).

FLNA p.Thr2016=

Q: How is Familial thoracic aortic aneurysm and aortic dissection inherited?

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

c.6048G>A · rs782745205 · VCV514722

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00436%, amr)

Conditions

familial thoracic aortic aneurysm and aortic dissection

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 -20	GERP -3.7
Overall
CADD	0.472	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00436% Admixed American · 2/45,910 alleles

Filtering AF 0.00202% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00172%

Overall 0.00264% 32/1,210,322 alleles · very rare exomes 26/1,097,802 · genomes 6/112,520 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00436%	22,955
South Asian	0.00352%	28,433
European (non-Finnish)	0.0029%	34,433
Remaining individualsnot grpmax-eligible	0.0021%	47,629
African / African-American	0.00174%	57,405

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: FLNA
Protein: p.Thr2016=
Coding: c.6048G>A
MANE Select: NM_001110556
dbSNP: rs782745205
Type: single nucleotide variant
Location: chrX:154353179 (GRCh38)
Structure: AlphaFold pLDDT 77.37 · 26 PDB
Residue 2016: a β-strand

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

Disease context

familial thoracic aortic aneurysm and aortic dissection — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: heterotopia, periventricular, X-linked dominant otopalatodigital syndrome type 2 Melnick-Needles syndrome frontometaphyseal dysplasia

For Familial thoracic aortic aneurysm and aortic dissection (Orphanet):

Inheritance: Autosomal dominant
Onset: Adolescent, Adult, Childhood

Similar variants

FLNA p.Thr2016Met Conflicting classifications of pathogenicity ★ ⚠ same residue
FLNA c.1066-1G>A Pathogenic/Likely pathogenic ★★ same condition
FLNA c.2022+1G>A Pathogenic ★★ same condition
FLNA c.4598+1G>A Pathogenic/Likely pathogenic ★★ same condition
FLNA c.5417-2A>G Likely pathogenic ★★ same condition
FLNA c.868+1G>A Likely pathogenic ★★ same condition
FLNA c.987+1G>A Likely pathogenic ★★ same condition
FLNA p.Ala1188Thr 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/flna-p-thr2016 (accessed [today's date]).

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