Is SERPINF1 p.Ile150Val (c.448A>G) pathogenic?

SERPINF1 p.Ile150Val (c.448A>G) is classified Benign/Likely benign in SERPINF1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-01-27). AlphaMissense: likely benign (0.076); Low-frequency (popmax 1.89%, afr).

How common is SERPINF1 p.Ile150Val (c.448A>G) in the general population?

SERPINF1 p.Ile150Val (c.448A>G) is low-frequency (popmax 1.89%, afr) (gnomAD).

What do computational predictors say about SERPINF1 p.Ile150Val (c.448A>G)?

AlphaMissense predicts likely benign (score 0.076) — an in-silico prediction, not a clinical call.

SERPINF1 p.Ile150Val

c.448A>G · rs62640873 · VCV773060

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.076 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.89%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.076	likely benign
REVEL	0.157	moderately benign-leaning
SaProt	LLR -5.89	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 2.4	GERP -0.88, phastCons 1
Regional constraint	o/e 1.04	unconstrained · MANE · 11 kb · p 0.37 · regional, not allelic
Overall
CADD	11.52	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.89% African / African-American · 1,416/75,034 alleles

Filtering AF 1.81% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.77%

Overall 0.0996% 1,607/1,612,824 alleles · low-frequency exomes 812/1,460,512 · genomes 795/152,312 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.89%	53
Admixed American	0.117%	857
Remaining individualsnot grpmax-eligible	0.111%	905
Middle Eastern	0.0352%	2,839
European (non-Finnish)	0.00398%	25,105
South Asian	0.00329%	30,357

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: SERPINF1
Protein: p.Ile150Val
Coding: c.448A>G
MANE Select: NM_002615
dbSNP: rs62640873
Type: single nucleotide variant
Location: chr17:1771880 (GRCh38)
Gene constraint: LOEUF 1.06 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 90.86 · 3 PDB

Full SERPINF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SERPINF1 p.Ile150Leu Uncertain significance ★ ⚠ same residue
SERPINF1 c.787-617G>A Likely pathogenic ★★ same type
SERPINF1 p.Arg303Ter Pathogenic/Likely pathogenic ★★ same type
SERPINF1 p.Arg99Ter Pathogenic ★★ same type
SERPINF1 p.Gln178Ter Pathogenic ★★ same type
SERPINF1 p.Gln185Ter Pathogenic ★★ same type
SERPINF1 p.Gln2Ter Likely pathogenic ★★ same type
SERPINF1 p.Gly270Ter 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/serpinf1-p-ile150val (accessed [today's date]).

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