Is TAF6 p.Ser563= (c.1689A>G) pathogenic?

TAF6 p.Ser563= (c.1689A>G) is classified Conflicting classifications of pathogenicity in TAF6 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-04-07). Ultra-rare (popmax 0.0674%, mid); Associated with Alazami-Yuan syndrome.

What condition is associated with TAF6 p.Ser563= (c.1689A>G)?

TAF6 p.Ser563= (c.1689A>G) is associated with Alazami-Yuan syndrome (ClinVar).

How common is TAF6 p.Ser563= (c.1689A>G) in the general population?

TAF6 p.Ser563= (c.1689A>G) is ultra-rare (popmax 0.0674%, mid) (gnomAD).

TAF6 p.Ser563=

c.1689A>G · rs768942294 · VCV730826

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0674%, mid)

Conditions

Alazami-Yuan syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.25	GERP -4.3, phastCons 0.44
Overall
CADD	3.631	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0674% Middle Eastern · 4/5,934 alleles

Filtering AF 0.023% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0138%

Overall 0.00304% 49/1,613,444 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0674%	1,483
Remaining individualsnot grpmax-eligible	0.0144%	6,939
Admixed American	0.00667%	14,981
European (non-Finnish)	0.00246%	40,685
South Asian	0.0022%	45,529
African / African-American	0.00134%	74,870

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: TAF6
Protein: p.Ser563=
Coding: c.1689A>G
MANE Select: NM_004722 · reported on NM_139315
dbSNP: rs768942294
Type: single nucleotide variant
Location: chr7:100107591 (GRCh38)

Full TAF6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Alazami-Yuan syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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/taf6-p-ser563 (accessed [today's date]).

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