Is ANKRD6 p.Ser579= (c.1737G>A) pathogenic?

ANKRD6 p.Ser579= (c.1737G>A) is classified Benign in ANKRD6 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-17). Common (popmax 91.6%, eas) — too common for a highly-penetrant pathogenic allele; Associated with ANKRD6-related disorder.

What condition is associated with ANKRD6 p.Ser579= (c.1737G>A)?

ANKRD6 p.Ser579= (c.1737G>A) is associated with ANKRD6-related disorder (ClinVar).

ANKRD6 p.Ser579=

Q: How common is ANKRD6 p.Ser579= (c.1737G>A) in the general population?

ANKRD6 p.Ser579= (c.1737G>A) is common (popmax 91.6%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.1737G>A · rs3210511 · VCV3059554

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 91.6%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

ANKRD6-related disorder

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 -0.87	GERP -3.7, phastCons 0.004
Overall
CADD	1.591	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 91.6% East Asian · 41,090/44,866 alleles

Filtering AF 90.8% ClinGen BA1/BS1 input FAF95, joint · FAF99 90.5%

Overall 49.9% 805,729/1,613,514 alleles · common exomes 723,968/1,461,364 · genomes 81,761/152,150 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	91.6%	1
Admixed American	68.4%	1
African / African-American	58%	2
Remaining individualsnot grpmax-eligible	51.7%	2
Finnishnot grpmax-eligible	49.1%	2
European (non-Finnish)	47.7%	2
Ashkenazi Jewishnot grpmax-eligible	46.6%	2
Middle Eastern	45.2%	2
South Asian	39.9%	3
Amishnot grpmax-eligible	36.5%	3

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: ANKRD6
Protein: p.Ser579=
Coding: c.1737G>A
MANE Select: NM_001242809
dbSNP: rs3210511
Type: single nucleotide variant
Location: chr6:89630557 (GRCh38)
Gene constraint: LOEUF 0.869 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.82
Residue 579: the 'disordered' region

Full ANKRD6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ANKRD6-related disorder

Similar variants

ANKRD6 p.Ala347= Benign same condition
ANKRD6 p.Ala550Thr Benign same condition
ANKRD6 p.Cys506= Benign same condition
ANKRD6 p.Gln122Glu Benign same condition
ANKRD6 p.Ile128Val Benign same condition
ANKRD6 p.Leu127= Likely benign same condition
ANKRD6 p.Pro636Leu Benign same condition
ANKRD6 p.Thr157= Likely 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/ankrd6-p-ser579 (accessed [today's date]).

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