Is FLT3 p.Asp358Val (c.1073A>T) pathogenic?

FLT3 p.Asp358Val (c.1073A>T) is classified Benign in FLT3 (ClinVar, Single submitter, 2 submitters; last evaluated 2019-12-31). AlphaMissense: likely benign (0.0895); Low-frequency (popmax 1.73%, eas).

How common is FLT3 p.Asp358Val (c.1073A>T) in the general population?

FLT3 p.Asp358Val (c.1073A>T) is low-frequency (popmax 1.73%, eas) (gnomAD).

What do computational predictors say about FLT3 p.Asp358Val (c.1073A>T)?

AlphaMissense predicts likely benign (score 0.0895) — an in-silico prediction, not a clinical call.

FLT3 p.Asp358Val

c.1073A>T · rs34172843 · VCV134452

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0895 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.73%, eas)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.0895	likely benign
REVEL	0.331	indeterminate
SaProt	LLR -4.25	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.1	GERP 2, phastCons 1
Regional constraint	o/e 0.90	unconstrained · MANE · 96 kb · p 0.00044 · regional, not allelic
Overall
CADD	20.4	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.73% East Asian · 774/44,846 alleles

Filtering AF 1.63% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.58%

Overall 0.0626% 1,008/1,610,464 alleles · low-frequency

Ancestry group	Frequency	1 in
East Asiangrpmax	1.73%	58
Ashkenazi Jewishnot grpmax-eligible	0.399%	251
Remaining individualsnot grpmax-eligible	0.0866%	1,155
South Asian	0.0286%	3,496
Middle Eastern	0.0165%	6,054
European (non-Finnish)	0.00297%	33,623

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: FLT3
Protein: p.Asp358Val
Coding: c.1073A>T
MANE Select: NM_004119
dbSNP: rs34172843
Type: single nucleotide variant
Location: chr13:28048407 (GRCh38)
Gene constraint: LOEUF 0.468 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.19 · 11 PDB
Residue 358: a UniProt-annotated variant site (in)

Full FLT3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

FLT3 c.1205+56C>T Benign ★★ same type
FLT3 c.1310-3T>C Benign ★★ same type
FLT3 c.1418+75A>G Benign ★★ same type
FLT3 c.1418+81A>G Benign ★★ same type
FLT3 c.1419-15T>C Benign ★★ same type
FLT3 c.1419-36T>A Benign ★★ same type
FLT3 c.1597+8A>G Likely benign ★★ same type
FLT3 c.165+118G>T Benign ★★ same type

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/flt3-p-asp358val (accessed [today's date]).

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