Is ANKRD17 p.Ile1679Val (c.5035A>G) pathogenic?

ANKRD17 p.Ile1679Val (c.5035A>G) is classified Likely benign in ANKRD17 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-08). AlphaMissense: likely benign (0.0587); Very rare (popmax 0.0012%, sas); Associated with Inborn genetic diseases.

What condition is associated with ANKRD17 p.Ile1679Val (c.5035A>G)?

ANKRD17 p.Ile1679Val (c.5035A>G) is associated with Inborn genetic diseases (ClinVar).

How common is ANKRD17 p.Ile1679Val (c.5035A>G) in the general population?

ANKRD17 p.Ile1679Val (c.5035A>G) is very rare (popmax 0.0012%, sas) (gnomAD).

What do computational predictors say about ANKRD17 p.Ile1679Val (c.5035A>G)?

AlphaMissense predicts likely benign (score 0.0587) — an in-silico prediction, not a clinical call.

ANKRD17 p.Ile1679Val

c.5035A>G · rs774552486 · VCV2324108

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0587 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0012%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0587	likely benign
REVEL	0.055	moderately benign-leaning
SaProt	LLR -5.21	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.11	GERP -3.7, phastCons 0.22
Regional constraint	o/e 0.97	unconstrained · MANE · 1,059 bp · p 0.77 · regional, not allelic
Overall
CADD	1.108	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 0.0012% South Asian · 1/83,414 alleles

Overall 0.00014% 2/1,425,454 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0012%	83,414
European (non-Finnish)	8.57e-05%	1,167,042

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: ANKRD17
Protein: p.Ile1679Val
Coding: c.5035A>G
MANE Select: NM_032217
dbSNP: rs774552486
Type: single nucleotide variant
Location: chr4:73097259 (GRCh38)
Gene constraint: LOEUF 0.118 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 53.73
Residue 1679: the 'disordered' region; a UniProt-annotated variant site (in cags)

Full ANKRD17 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

ANKRD17 p.Ile1679Leu Uncertain significance ★ ⚠ same residue
ANKRD17 p.Arg1712His Uncertain significance ★★ ⚠ same condition
ANKRD17 p.Arg418Gln Uncertain significance ★★ ⚠ same condition
ANKRD17 p.Arg52Cys Uncertain significance ★★ ⚠ same condition
ANKRD17 p.Cys1690Tyr Uncertain significance ★★ ⚠ same condition
ANKRD17 p.Gln907Pro Uncertain significance ★★ ⚠ same condition
ANKRD17 p.Glu1508Asp Uncertain significance ★★ ⚠ same condition
ANKRD17 p.Glu1526Ala 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/ankrd17-p-ile1679val (accessed [today's date]).

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