Is ANK3 p.Val1713Ile (c.5137G>A) pathogenic?

ANK3 p.Val1713Ile (c.5137G>A) is classified Conflicting classifications of pathogenicity in ANK3 (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2026-01-01). AlphaMissense: likely benign (0.0914); Low-frequency (popmax 1.05%, sas); Associated with Inborn genetic diseases.

What condition is associated with ANK3 p.Val1713Ile (c.5137G>A)?

ANK3 p.Val1713Ile (c.5137G>A) is associated with Inborn genetic diseases (ClinVar).

How common is ANK3 p.Val1713Ile (c.5137G>A) in the general population?

ANK3 p.Val1713Ile (c.5137G>A) is low-frequency (popmax 1.05%, sas) (gnomAD).

What do computational predictors say about ANK3 p.Val1713Ile (c.5137G>A)?

AlphaMissense predicts likely benign (score 0.0914) — an in-silico prediction, not a clinical call.

ANK3 p.Val1713Ile

c.5137G>A · rs544357242 · VCV426668

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 4 submitters

AlphaMissense

likely benign

0.0914 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.05%, sas)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0914	likely benign
REVEL	0.142	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6	GERP 4.6, phastCons 1
Regional constraint	o/e 0.86	unconstrained · MANE · 7,641 bp · p 6.9e-05 · regional, not allelic
Overall
CADD	21.6	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 1.05% South Asian · 953/91,082 alleles

Filtering AF 0.991% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.969%

Overall 0.0611% 986/1,614,126 alleles · low-frequency

Ancestry group	Frequency	1 in
South Asiangrpmax	1.05%	96
Remaining individualsnot grpmax-eligible	0.0464%	2,156
Middle Eastern	0.0165%	6,062
East Asian	0.00223%	44,880
European (non-Finnish)	0.000169%	590,002

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: ANK3
Protein: p.Val1713Ile
Coding: c.5137G>A
MANE Select: NM_020987
dbSNP: rs544357242
Type: single nucleotide variant
Location: chr10:60075744 (GRCh38)
Gene constraint: LOEUF 0.16 · pLI 1.00 (gnomAD)

Full ANK3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ANK3 p.Val1713Leu Uncertain significance ★ ⚠ same residue
ANK3 p.Ala1534Val Uncertain significance ★★ same condition
ANK3 p.Ala218Thr Uncertain significance ★★ same condition
ANK3 p.Ala259Thr Uncertain significance ★★ same condition
ANK3 p.Ala324Gly Uncertain significance ★★ ⚠ same condition
ANK3 p.Ala3262Val Uncertain significance ★★ ⚠ same condition
ANK3 p.Ala540Thr Uncertain significance ★★ same condition
ANK3 p.Arg1012Cys 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/ank3-p-val1713ile (accessed [today's date]).

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