Is BIRC6 p.Gln1771= (c.5313A>G) pathogenic?

BIRC6 p.Gln1771= (c.5313A>G) is classified Benign in BIRC6 (ClinVar, No assertion criteria, 2 submitters; last evaluated 2019-11-04). Common (popmax 14.6%, eas) — too common for a highly-penetrant pathogenic allele; Associated with BIRC6-related disorder.

What condition is associated with BIRC6 p.Gln1771= (c.5313A>G)?

BIRC6 p.Gln1771= (c.5313A>G) is associated with BIRC6-related disorder (ClinVar).

BIRC6 p.Gln1771=

Q: How common is BIRC6 p.Gln1771= (c.5313A>G) in the general population?

BIRC6 p.Gln1771= (c.5313A>G) is common (popmax 14.6%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.5313A>G · rs35682129 · VCV3059999

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 14.6%, eas) — too common for a highly-penetrant pathogenic allele

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 0.005	GERP -5.5, phastCons 0.043
Overall
CADD	5.892	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 14.6% East Asian · 6,485/44,496 alleles

Filtering AF 14.3% ClinGen BA1/BS1 input FAF95, joint · FAF99 14.2%

Overall 7.44% 119,233/1,602,818 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	14.6%	7
Amishnot grpmax-eligible	13.1%	8
Admixed American	9.51%	11
Middle Eastern	9.5%	11
European (non-Finnish)	7.76%	13
Remaining individualsnot grpmax-eligible	7.14%	14
Finnishnot grpmax-eligible	6.89%	15
Ashkenazi Jewishnot grpmax-eligible	6.23%	16
South Asian	4.07%	25
African / African-American	1.51%	66

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.Gln1771=
Coding: c.5313A>G
MANE Select: NM_016252
dbSNP: rs35682129
Type: single nucleotide variant
Location: chr2:32465121 (GRCh38)
Gene constraint: LOEUF 0.213 · pLI 1.00 (gnomAD)

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

Disease context

BIRC6-related disorder

Similar variants

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
BIRC6 p.Asp3819Tyr 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-gln1771 (accessed [today's date]).

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