Is SERPING1 p.Val56fs (c.166del) pathogenic?

SERPING1 p.Val56fs (c.166del) is classified Pathogenic in SERPING1 (ClinVar, Single submitter, 1 submitter; last evaluated 2017-11-06). No gnomAD frequency available for this variant.

How common is SERPING1 p.Val56fs (c.166del) in the general population?

SERPING1 p.Val56fs (c.166del) is no gnomAD frequency available for this variant (gnomAD).

SERPING1 p.Val56fs

c.166del · rs1554994909 · VCV503648

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 3 of 8
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -1.4	GERP -4.6

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: SERPING1
Protein: p.Val56fs
Coding: c.166del
MANE Select: NM_000062
dbSNP: rs1554994909
Type: Deletion
Location: chr11:57599993 (GRCh38)
Gene constraint: LOEUF 0.278 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 80.63 · 5 PDB
Residue 56: a UniProt-annotated variant site (in)

Full SERPING1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SERPING1 p.Val56Ala Benign ★★ same residue
SERPING1 p.Val56Ile Uncertain significance ★ ⚠ same residue
SERPING1 p.His314fs Pathogenic ★★ same type
SERPING1 p.Leu386fs Pathogenic/Likely pathogenic ★★ same type
SERPING1 p.Phe55fs Pathogenic ★★ same type
SERPING1 p.Ser283fs Pathogenic ★★ same type
SERPING1 p.Val332fs Pathogenic ★★ same type
SERPING1 c.1029+1del Pathogenic ★ same type

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-val56fs (accessed [today's date]).

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