Is SERPING1 p.Ala156= (c.468C>T) pathogenic?

SERPING1 p.Ala156= (c.468C>T) is classified Benign/Likely benign in SERPING1 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-01-24). Rare (popmax 0.299%, nfe); Associated with Inborn genetic diseases.

What condition is associated with SERPING1 p.Ala156= (c.468C>T)?

SERPING1 p.Ala156= (c.468C>T) is associated with Inborn genetic diseases, hereditary angioedema type 1 (ClinVar).

How common is SERPING1 p.Ala156= (c.468C>T) in the general population?

SERPING1 p.Ala156= (c.468C>T) is rare (popmax 0.299%, nfe) (gnomAD).

SERPING1 p.Ala156=

c.468C>T · rs150601964 · VCV305024

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

rare (popmax 0.299%, nfe)

Conditions

Inborn genetic diseases

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 -0.27	GERP -2.4, phastCons 0.19
Overall
CADD	9.9	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.299% European (non-Finnish) · 3,523/1,180,026 alleles

Filtering AF 0.29% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.287%

Overall 0.236% 3,810/1,613,996 alleles · rare exomes 3,607/1,461,716 · genomes 203/152,280 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.299%	335
Remaining individualsnot grpmax-eligible	0.259%	386
South Asian	0.0604%	1,656
Admixed American	0.0467%	2,143
African / African-American	0.04%	2,501
Finnishnot grpmax-eligible	0.0172%	5,822
Middle Eastern	0.0169%	5,926

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: SERPING1
Protein: p.Ala156=
Coding: c.468C>T
MANE Select: NM_000062
dbSNP: rs150601964
Type: single nucleotide variant
Location: chr11:57600295 (GRCh38)
Gene constraint: LOEUF 0.278 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 80.63 · 5 PDB
Residue 156: an α-helix

Full SERPING1 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

Also linked: hereditary angioedema type 1

Similar variants

SERPING1 p.Ala156Thr Likely benign ★ same residue
SERPING1 c.1030-1G>T Pathogenic ★★ same condition
SERPING1 c.51+1G>T Pathogenic ★★ same condition
SERPING1 c.51+3A>C Pathogenic/Likely pathogenic ★★ same condition
SERPING1 c.51+3A>G Pathogenic ★★ same condition
SERPING1 c.52-1G>A Pathogenic ★★ same condition
SERPING1 c.550+1G>A Pathogenic ★★ same condition
SERPING1 c.551-1G>C Pathogenic/Likely pathogenic ★★ 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/serping1-p-ala156 (accessed [today's date]).

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