Is BIRC6 p.Asn4354= (c.13062T>C) pathogenic?

BIRC6 p.Asn4354= (c.13062T>C) is classified Likely benign in BIRC6 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-09-18). Ultra-rare (popmax 0.0962%, afr); Associated with BIRC6-related disorder.

What condition is associated with BIRC6 p.Asn4354= (c.13062T>C)?

BIRC6 p.Asn4354= (c.13062T>C) is associated with BIRC6-related disorder (ClinVar).

How common is BIRC6 p.Asn4354= (c.13062T>C) in the general population?

BIRC6 p.Asn4354= (c.13062T>C) is ultra-rare (popmax 0.0962%, afr) (gnomAD).

BIRC6 p.Asn4354=

c.13062T>C · rs149447533 · VCV3040028

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0962%, afr)

Conditions

BIRC6-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 -1.5	GERP -3.8
Overall
CADD	1.86	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0962% African / African-American · 71/73,808 alleles

Filtering AF 0.0782% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0716%

Overall 0.00585% 89/1,521,466 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0962%	1,040
Remaining individualsnot grpmax-eligible	0.0122%	8,222
Admixed American	0.0085%	11,763
European (non-Finnish)	0.000538%	185,913

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: BIRC6
Protein: p.Asn4354=
Coding: c.13062T>C
MANE Select: NM_016252
dbSNP: rs149447533
Type: single nucleotide variant
Location: chr2:32549399 (GRCh38)
Gene constraint: LOEUF 0.213 · pLI 1.00 (gnomAD)
Residue 4354: a β-strand

Full BIRC6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

BIRC6-related disorder

Similar variants

BIRC6 p.Asn4354His Uncertain significance ★ ⚠ same residue
BIRC6 p.Gln853Arg Uncertain significance ★★ ⚠ same condition
BIRC6 p.Glu4506Asp Uncertain significance ★★ ⚠ same condition
BIRC6 p.Arg1075Gln Uncertain significance ★ ⚠ same condition
BIRC6 p.Asp386Glu Uncertain significance ★ same condition
BIRC6 p.Asp673His Uncertain significance ★ same condition
BIRC6 p.Ser1258Ala Uncertain significance ★ ⚠ same condition
BIRC6 p.Ser3427Phe 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/birc6-p-asn4354 (accessed [today's date]).

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